[OMPI users] WRF Problem running in Parallel on multiple nodes (cluster)
Hello, I am able to run WRFV3.2.1 using mpirun on multiple cores of single machine, but when I want to run it across multiple nodes in cluster using hostlist then I get error, The compute nodes are mounted with the master node during boot using NFS. I get following error. Please help. [root@pmd02 em_real]# mpirun -np 10 -hostfile /home/pmdtest/hostlist ./real.exe bash: orted: command not found bash: orted: command not found -- A daemon (pid 22006) died unexpectedly with status 127 while attempting to launch so we are aborting. There may be more information reported by the environment (see above). This may be because the daemon was unable to find all the needed shared libraries on the remote node. You may set your LD_LIBRARY_PATH to have the location of the shared libraries on the remote nodes and this will automatically be forwarded to the remote nodes. -- -- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -- mpirun: clean termination accomplished -- Syed Ahsan Ali Bokhari Electronic Engineer (EE) Research & Development Division Pakistan Meteorological Department H-8/4, Islamabad. Phone # off +92518358714 Cell # +923155145014
Re: [OMPI users] is there an equiv of iprove for bcast?
From: Randolph Pullen Subject: Re: Re: [OMPI users] is there an equiv of iprove for bcast? To: us...@open-mpi.or Received: Monday, 2 May, 2011, 12:53 PM Non blocking Bcasts or tests would do it.I currently have the clearing-house solution working but it is unsatisfying because of its serial node. - As it scales it will overload this node. The problem rephrased:Instead of n*2 processes, I am having to use n*2+1 with the extra process serially receiving listener messages on behalf of the workers before transmitting these messages to workers in its comm_group. Is there a way to Bcast directly from each listener to the worker pool? (listeners must monitor their ports most of the time and cant participate in global bcasts)Not knowing which listener is going to transmit prevents the correct comm_group being used with Bcast calls. --- On Sat, 30/4/11, Jeff Squyres wrote: From: Jeff Squyres Subject: Re: [OMPI users] is there an equiv of iprove for bcast? To: randolph_pul...@yahoo.com.au, "Open MPI Users" Received: Saturday, 30 April, 2011, 7:17 AM On Apr 29, 2011, at 1:21 AM, Randolph Pullen wrote: > I am having a design issue: > My server application has 2 processes per node, 1 listener and 1 worker. > Each listener monitors a specified port for incoming TCP connections with the > goal that on receipt of a request it will distribute it over the workers in a > SIMD fashion. > > My problem is this: how can I get the workers to accept work from any of the > listeners? > Making a separate communicator does not help as the sender is unknown. Other > than making a serial 'clearing house' process I cant think of a way - Iprobe for Bcast would be useful. I'm not quite sure I understand your question. There currently is no probe for collectives, but MPI-3 has non-blocking collectives which you could MPI_Test for. There's a 3rd party library implementation called libNBC (non-blocking collectives) that you could use until such things become natively available. -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] problems with the -xterm option
Launching xterm by mpirun onto a remote platform without a command simply opens a xterm-window which sits there until you type exit into it or close it by pressing on the frame's close button. (of course only if the display is forwarded to the local machine) On Mon, May 2, 2011 at 4:30 PM, Ralph Castain wrote: > > On May 2, 2011, at 8:21 AM, jody wrote: > >> Hi >> Well, the difference is that one time i call the application >> 'HelloMPI' with the '--xterm' option, >> whereas in my previous mail i am calling the application 'xterm' >> (without the '--xterm' option) > > Ah, well that might explain it. I don't know how xterm would react to just > being launched by mpirun onto a remote platform without any command to run. I > can't explain what the plm verbosity has to do with anything, though. > >> Jody >> >> On Mon, May 2, 2011 at 4:08 PM, Ralph Castain wrote: >>> >>> On May 2, 2011, at 7:56 AM, jody wrote: >>> Hi Ralph Thank You for doing the fix. Do you perhaps also have an idea what is going on when i try to start xterm (or probably an other X application) on a remote host? In this case it is not enough to specify the '--leave-session-attached' option. These calls won't open any xterms mpirun -np 4 -host squid_0 -mca plm_rsh_agent "ssh -Y" -mca plm_base_verbose 1 xterm mpirun -np 4 -host squid_0 -mca plm_rsh_agent "ssh -Y" --leave-session-attached xterm mpirun -np 4 -host squid_0 -mca plm_rsh_agent "ssh -Y" -mca odls_base_verbose 5 xterm mpirun -np 4 -host squid_0 -mca plm_rsh_agent "ssh -Y" -mca odls_base_verbose 5 --leave-session-attached xterm But this will open the xterms: mpirun -np 4 -host squid_0 -mca plm_rsh_agent "ssh -Y" -mca plm_base_verbose 1 --leave-session-attached xterm Any verbosity level > 0 will open xterms, but with ' -mca plm_base_verbose 0' there are again no xterms. >>> >>> No earthly idea...this seems to contradict what you had below. You said you >>> were seeing the xterms with this cmd line: >>> >> I just found that everything works as expected if i use the the >> '--leave-session-attached' option (without the debug options): >> jody@chefli ~/share/neander $ mpirun -np 4 -host squid_0 -mca >> plm_rsh_agent "ssh -Y" --leave-session-attached --xterm 0,1,2,3! >> ./HelloMPI >> The xterms are also opened if i do not use the '!' hold option. > >>> >>> Did I miss something? >>> >>> Thank You Jody On Mon, May 2, 2011 at 2:29 PM, Ralph Castain wrote: > > On May 2, 2011, at 2:34 AM, jody wrote: > >> Hi Ralph >> >> I rebuilt open MPI 1.4.2 with the debug option on both chefli and >> squid_0. >> The results are interesting! >> >> I wrote a small HelloMPI app which basically calls usleep for a pause >> of 5 seconds. >> >> Now calling it as i did before, no MPI errors appear anymore, only the >> display problems: >> jody@chefli ~/share/neander $ mpirun -np 1 -host squid_0 -mca >> plm_rsh_agent "ssh -Y" --xterm 0 ./HelloMPI >> /usr/bin/xterm Xt error: Can't open display: localhost:10.0 >> >> When i do the same call *with* the debug option, the xterm appears and >> shows the output of HelloMPI! >> I attach the output in ompidbg_1.txt (It also works if i call with >> '-np 4' and '--xterm 0,1,2,3' > > Good! > >> >> Calling hostname the same way does not open an xterm (cf. ompidbg_2.txt). >> >> If i use the hold-option, the xterm appears with the output of >> 'hostrname' (cf. ompidbg_3.txt) >> The xterm opens after the line "launch complete for job..." has been >> written (line 59) > > Okay, that's also expected. Like I said, without the "hold", the output > is generated so quickly that the window just flashes at best. I've had > similar experiences - hence the "hold" option. > >> >> I just found that everything works as expected if i use the the >> '--leave-session-attached' option (without the debug options): >> jody@chefli ~/share/neander $ mpirun -np 4 -host squid_0 -mca >> plm_rsh_agent "ssh -Y" --leave-session-attached --xterm 0,1,2,3! >> ./HelloMPI >> The xterms are also opened if i do not use the '!' hold option. > > Okay, I can understand why. The --leave-session-attached option just > tells mpirun to not daemonize the backend daemons - thus leaving the ssh > session alive. The debug options do the same thing, but turn on all the > debug output. > > The problem is that if you don't leave the ssh session alive, then the > xterm has no way back to your screen. By daemonizing, we severe that > connection. > > What I should do (and maybe used to do, but it got removed) is > automatically turn "on" the leave-session-attached option if you give > --xterm. I ca
Re: [OMPI users] WRF Problem running in Parallel on multiple nodes (cluster)
The error message is telling you the problem. You don't have your remote path set so it can find the OMPI installation on the remote hosts. Look at the OMPI FAQ section for more info if you are unsure how to set paths on remote hosts. On May 3, 2011, at 2:04 AM, Ahsan Ali wrote: > Hello, > > I am able to run WRFV3.2.1 using mpirun on multiple cores of single machine, > but when I want to run it across multiple nodes in cluster using hostlist > then I get error, The compute nodes are mounted with the master node during > boot using NFS. I get following error. Please help. > > [root@pmd02 em_real]# mpirun -np 10 -hostfile /home/pmdtest/hostlist > ./real.exe > bash: orted: command not found > bash: orted: command not found > -- > A daemon (pid 22006) died unexpectedly with status 127 while attempting > to launch so we are aborting. > > There may be more information reported by the environment (see above). > > This may be because the daemon was unable to find all the needed shared > libraries on the remote node. You may set your LD_LIBRARY_PATH to have the > location of the shared libraries on the remote nodes and this will > automatically be forwarded to the remote nodes. > -- > -- > mpirun noticed that the job aborted, but has no info as to the process > that caused that situation. > -- > mpirun: clean termination accomplished > > > -- > Syed Ahsan Ali Bokhari > Electronic Engineer (EE) > > Research & Development Division > Pakistan Meteorological Department H-8/4, Islamabad. > Phone # off +92518358714 > Cell # +923155145014 > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] Building openmpi with PGI 11.4: won't find torque??
It should search both tmdir/lib and tmdir/lib64 by default, IIRC. Please send your config.log (please compress); it'll contain the specific reason why configure didn't find libtorque. On May 2, 2011, at 10:21 PM, Ralph Castain wrote: > It's probably looking for the torque lib in lib instead of lib64. There > should be a configure option to tell it --with-tm-libdir or something like > that - check "configure -h" > > > On May 2, 2011, at 6:22 PM, Jim Kusznir wrote: > >> Hi all: >> >> I'm trying to build openmpi 1.4.3 against PGI 11.4 on my Rocks 5.1 >> system. My "tried and true" build command for OpenMPI is: >> >> CC=pgcc CXX=pgCC F77=pgf77 FC=pgf90 rpmbuild -bb --define >> 'install_in_opt 1' --define 'install_modulefile 1' --define >> 'modules_rpm_name environment-modules' --define 'build_all_in_one_rpm >> 0' --define 'configure_options --with-tm=/opt/torque' --define '_name >> openmpi-pgi2011' --define 'use_default_rpm_opt_flags 0' >> openmpi-1.4.3.spec >> >> This is what I've used to build openmpi 1.4.3 for gcc and against PGI >> 8.x (our last version of PGI installed). This time, its not working, >> though, and with what I consider to be a very strange failure point: >> >> --- MCA component plm:tm (m4 configuration macro) >> checking for MCA component plm:tm compile mode... dso >> checking --with-tm value... sanity check ok (/opt/torque) >> checking for pbs-config... /opt/torque/bin/pbs-config >> checking tm.h usability... yes >> checking tm.h presence... yes >> checking for tm.h... yes >> checking for tm_finalize... no >> checking tm.h usability... yes >> checking tm.h presence... yes >> checking for tm.h... yes >> looking for library in lib >> checking for tm_init in -lpbs... no >> looking for library in lib64 >> checking for tm_init in -lpbs... no >> looking for library in lib >> checking for tm_init in -ltorque... no >> looking for library in lib64 >> checking for tm_init in -ltorque... no >> configure: error: TM support requested but not found. Aborting >> error: Bad exit status from /var/tmp/rpm-tmp.7564 (%build) >> >> >> However, /opt/torque/ is present. /opt/torque/bin/pbs-config returns: >> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --prefix >> /opt/torque >> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --package >> pbs >> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --version >> 2.3.0 >> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --libs >> -L/opt/torque/lib64 -ltorque -Wl,--rpath -Wl,/opt/torque/lib64 >> >> and /opt/torque/lib64 does have: >> [root@aeolus modulefiles]# ls /opt/torque/lib64 >> libtorque.a libtorque.la libtorque.so libtorque.so.2 libtorque.so.2.0.0 >> >> so I'm a bit dumbfounded as to why configure doesn't "find" torque >> support...Any suggestions? >> >> --Jim >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] OpenMPI LS-DYNA Connection refused
A little more clarification: 1. Simulations that fail always seem to fail? 2. Does the same simulation always fail between the same processes (how about nodes)? I thought you said no previously. 3. Did the mpi_preconnect_mpi help any? 4. Is there any informational messages in the /var/log/messages file around or before the abort? 5. Have you tried netstat -s 1 while the program is running on one of the nodes that fail and see if you are getting any of the failure type events spiking? The error code coming back from MPI_Abort seems really odd. I am curious whether the connection refused is a result of the abort or what? --td On 05/02/2011 03:40 PM, Robert Walters wrote: I've attached the typical error message I've been getting. This is from a run I initiated this morning. The first few lines or so are related to the LS-DYNA program and are just there to let you know its running successfully for an hour and a half. What's interesting is this doesn't happen on every job I run, and will recur for the same simulation. For instance, Simulation A will run for 40 hours, and complete successfully. Simulation B will run for 6 hours, and die from an error. Any further attempts to run simulation B will always end from an error. This makes me think there is some kind of bad calculation happening that OpenMPI doesn't know how to handle, or LS-DYNA doesn't know how to pass to OpenMPI. On the other hand, this particular simulation is one of those "benchmarks" and everyone runs it. I should not be getting errors from the FE code itself. Odd... I think I'll try this as an SMP job as well as an MPP job over a single node and see if the issue continues. That way I can figure out if its OpenMPI related or FE code related, but as I mentioned, I don't think it is FE code related since others have successfully run this particular benchmarking simulation. *_Error Message:_* Parallel execution with 56 MPP proc NLQ used/max 152/ 152 Start time 05/02/2011 10:02:20 End time 05/02/2011 11:24:46 Elapsed time4946 seconds( 1 hours 22 min. 26 sec.) for9293 cycles E r r o r t e r m i n a t i o n -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1525207032. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- connect to address xx.xxx.xx.xxx port 544: Connection refused connect to address xx.xxx.xx.xxx port 544: Connection refused trying normal rsh (/usr/bin/rsh) -- mpirun has exited due to process rank 0 with PID 24488 on node allision exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- Regards, Robert Walters *From:*users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] *On Behalf Of *Terry Dontje *Sent:* Monday, May 02, 2011 2:50 PM *To:* us...@open-mpi.org *Subject:* Re: [OMPI users] OpenMPI LS-DYNA Connection refused On 05/02/2011 02:04 PM, Robert Walters wrote: Terry, I was under the impression that all connections are made because of the nature of the program that OpenMPI is invoking. LS-DYNA is a finite element solver and for any given simulation I run, the cores on each node must constantly communicate with one another to check for various occurrences (contact with various pieces/parts, updating nodal coordinates, etc...). You might be right, the connections might have been established but the error message you state (connection refused) seems out of place if the connection was already established. Was there more error messages from OMPI other than "connection refused"? If so could you possibly provide that output to us, maybe it will give us a hint where in the library things are messing up. I've run the program using --mca mpi_preconnect_mpi 1 and the simulation has started itself up successfully which I think means that the mpi_preconnect passed since all of the child processes have started up on each individual node. Thanks for the suggestion though, it's a good place to start. Yeah, it possibly could be telling if things do work with this setting. I've been worried (though I have no basis for it) that messages may be getting queued up and hitting some kind of ceiling or timeout. As a finite element code, I think the communication occurs on a large scale. Lots of very small packets going back and forth quickly. A few studies have been done by the High Performance Computing Advi
Re: [OMPI users] OpenMPI LS-DYNA Connection refused
Looking at your output more the below "Connect to address" doesn't match any messages I see in the source code. Also "trying normal /usr/bin/rsh" looks odd to me. You may want to set the mca parameter mpi_abort_delay and attach a debugger to the abortive process and dump out a stack trace. That should give a better idea where the failure is being triggered. You can look at http://www.open-mpi.org/faq/?category=debugging question 4 for more info on the parameter. --td On 05/02/2011 03:40 PM, Robert Walters wrote: I've attached the typical error message I've been getting. This is from a run I initiated this morning. The first few lines or so are related to the LS-DYNA program and are just there to let you know its running successfully for an hour and a half. What's interesting is this doesn't happen on every job I run, and will recur for the same simulation. For instance, Simulation A will run for 40 hours, and complete successfully. Simulation B will run for 6 hours, and die from an error. Any further attempts to run simulation B will always end from an error. This makes me think there is some kind of bad calculation happening that OpenMPI doesn't know how to handle, or LS-DYNA doesn't know how to pass to OpenMPI. On the other hand, this particular simulation is one of those "benchmarks" and everyone runs it. I should not be getting errors from the FE code itself. Odd... I think I'll try this as an SMP job as well as an MPP job over a single node and see if the issue continues. That way I can figure out if its OpenMPI related or FE code related, but as I mentioned, I don't think it is FE code related since others have successfully run this particular benchmarking simulation. *_Error Message:_* Parallel execution with 56 MPP proc NLQ used/max 152/ 152 Start time 05/02/2011 10:02:20 End time 05/02/2011 11:24:46 Elapsed time4946 seconds( 1 hours 22 min. 26 sec.) for9293 cycles E r r o r t e r m i n a t i o n -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1525207032. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- connect to address xx.xxx.xx.xxx port 544: Connection refused connect to address xx.xxx.xx.xxx port 544: Connection refused trying normal rsh (/usr/bin/rsh) -- mpirun has exited due to process rank 0 with PID 24488 on node allision exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- Regards, Robert Walters *From:*users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] *On Behalf Of *Terry Dontje *Sent:* Monday, May 02, 2011 2:50 PM *To:* us...@open-mpi.org *Subject:* Re: [OMPI users] OpenMPI LS-DYNA Connection refused On 05/02/2011 02:04 PM, Robert Walters wrote: Terry, I was under the impression that all connections are made because of the nature of the program that OpenMPI is invoking. LS-DYNA is a finite element solver and for any given simulation I run, the cores on each node must constantly communicate with one another to check for various occurrences (contact with various pieces/parts, updating nodal coordinates, etc...). You might be right, the connections might have been established but the error message you state (connection refused) seems out of place if the connection was already established. Was there more error messages from OMPI other than "connection refused"? If so could you possibly provide that output to us, maybe it will give us a hint where in the library things are messing up. I've run the program using --mca mpi_preconnect_mpi 1 and the simulation has started itself up successfully which I think means that the mpi_preconnect passed since all of the child processes have started up on each individual node. Thanks for the suggestion though, it's a good place to start. Yeah, it possibly could be telling if things do work with this setting. I've been worried (though I have no basis for it) that messages may be getting queued up and hitting some kind of ceiling or timeout. As a finite element code, I think the communication occurs on a large scale. Lots of very small packets going back and forth quickly. A few studies have been done by the High Performance Computing Advisory Council (http://www.hpcadvisorycouncil.com/pdf/LS-DYNA%20_analysis.pdf) and they've suggested that LS-DYNA communicates at very, very high rates (Not sure
Re: [OMPI users] btl_openib_cpc_include rdmacm questions
Brock Palen writes: > We managed to have another user hit the bug that causes collectives (this > time MPI_Bcast() ) to hang on IB that was fixed by setting: > > btl_openib_cpc_include rdmacm Could someone explain this? We also have problems with collective hangs with openib/mlx4 (specifically in IMB), but not with psm, and I couldn't see any relevant issues filed. However, rdmacm isn't an available value for that parameter with our 1.4.3 or 1.5.3 installations, only oob (not that I understand what these things are...).
[OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Dear Sir/Madam I want to build openmpi for use with INTEL compilers (version 11.1) on my Ubuntu 10.10 x64 system. I am using the guidelines from http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-open-mpi-with-the-intel-compilers/ and specifically the following instructions: ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort ... output of configure ... make all install ... output of build and installation ... The result is shown below. As can be seen it was unsuccessful. I'll appreciate some guidance here as I am nearing the deadline for a project that is part of my research for my PhD. Thanks in advance. steph@sjb-linux:/src/openmpi-1.4.3$ ./configure --prefix=/opt/openmpi-1.4.3 CC=icc CXX=icpc F77=ifort FC=ifort checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes : command not foundconfig/missing: line 3: : command not foundconfig/missing: line 5: : command not foundconfig/missing: line 9: : command not foundconfig/missing: line 14: : command not foundconfig/missing: line 19: : command not foundconfig/missing: line 24: : command not foundconfig/missing: line 29: /src/openmpi-1.4.3/config/missing: line 49: syntax error near unexpected token `'n 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar == Configuring Open MPI *** Checking versions : integer expression expected 3 : integer expression expected 0 .4ecking Open MPI version... 1 checking Open MPI release date... Oct 05, 2010 checking Open MPI Subversion repository version... r23834 : integer expression expected 3 : integer expression expected 0 .4ecking Open Run-Time Environment version... 1 checking Open Run-Time Environment release date... Oct 05, 2010 checking Open Run-Time Environment Subversion repository version... r23834 : integer expression expected 3 : integer expression expected 0 .4ecking Open Portable Access Layer version... 1 checking Open Portable Access Layer release date... Oct 05, 2010 checking Open Portable Access Layer Subversion repository version... r23834 : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found *** Initialization, setup configure: builddir: /src/openmpi-1.4.3 configure: srcdir: /src/openmpi-1.4.3 configure: error: cannot run /bin/sh config/config.sub steph@sjb-linux:/src/openmpi-1.4.3$ make all install make: *** No rule to make target `all'. Stop. steph@sjb-linux:/src/openmpi-1.4.3$ make install make: *** No rule to make target `install'. Stop. steph@sjb-linux:/src/openmpi-1.4.3$ Regards Steph Bredenhann -- This message was sent by Adept Internet's webmail. http://www.adept.co.za/
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Your output appears jumbled. Can you send all the data listed here: http://www.open-mpi.org/community/help/ On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: > Dear Sir/Madam > > I want to build openmpi for use with INTEL compilers (version 11.1) on my > Ubuntu > 10.10 x64 system. I am using the guidelines from > http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-open-mpi-with-the-intel-compilers/ > and specifically the following instructions: > > > ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort > ... output of configure ... > make all install > ... output of build and installation ... > > The result is shown below. As can be seen it was unsuccessful. I'll appreciate > some guidance here as I am nearing the deadline for a project that is part of > my research for my PhD. > > Thanks in advance. > > steph@sjb-linux:/src/openmpi-1.4.3$ ./configure --prefix=/opt/openmpi-1.4.3 > CC=icc CXX=icpc F77=ifort FC=ifort > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > : command not foundconfig/missing: line 3: > : command not foundconfig/missing: line 5: > : command not foundconfig/missing: line 9: > : command not foundconfig/missing: line 14: > : command not foundconfig/missing: line 19: > : command not foundconfig/missing: line 24: > : command not foundconfig/missing: line 29: > /src/openmpi-1.4.3/config/missing: line 49: syntax error near unexpected token > `'n > 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in > configure: WARNING: `missing' script is too old or missing > checking for a thread-safe mkdir -p... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > > > == Configuring Open MPI > > > *** Checking versions > : integer expression expected 3 > : integer expression expected 0 > .4ecking Open MPI version... 1 > checking Open MPI release date... Oct 05, 2010 > checking Open MPI Subversion repository version... r23834 > : integer expression expected 3 > : integer expression expected 0 > .4ecking Open Run-Time Environment version... 1 > checking Open Run-Time Environment release date... Oct 05, 2010 > checking Open Run-Time Environment Subversion repository version... r23834 > : integer expression expected 3 > : integer expression expected 0 > .4ecking Open Portable Access Layer version... 1 > checking Open Portable Access Layer release date... Oct 05, 2010 > checking Open Portable Access Layer Subversion repository version... r23834 > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > : command not found > > *** Initialization, setup > configure: builddir: /src/openmpi-1.4.3 > configure: srcdir: /src/openmpi-1.4.3 > configure: error: cannot run /bin/sh config/config.sub > steph@sjb-linux:/src/openmpi-1.4.3$ make all install > make: *** No rule to make target `all'. Stop. > steph@sjb-linux:/src/openmpi-1.4.3$ make install > make: *** No rule to make target `install'. Stop. > steph@sjb-linux:/src/openmpi-1.4.3$ > > > Regards > > Steph Bredenhann > > > > > > > -- > This message was sent by Adept Internet's webmail. > http://www.adept.co.za/ > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
[OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Dear Sir/Madam I want to build openmpi for use with INTEL compilers (version 11.1) on my Ubuntu 10.10 x64 system. The details are attached. Your assistance will be appreciated. Regards -- Steph Bredenhann Pr.Eng Pr.CPM -- This message was sent by Adept Internet's webmail. http://www.adept.co.za/ ompi-output.tar.bz2 Description: application/bzip
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Thanks for the speedy reply. The required file with information is attached. I first thought I must send the file to openmpi again, sorry if that was wrong. Thanks -- Steph Bredenhann Pr.Eng Pr.CPM Quoting Jeff Squyres : > Your output appears jumbled. Can you send all the data listed here: > > http://www.open-mpi.org/community/help/ > > On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: > > > Dear Sir/Madam > > > > I want to build openmpi for use with INTEL compilers (version 11.1) on my > Ubuntu > > 10.10 x64 system. I am using the guidelines from > > > http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-open-mpi-with-the-intel-compilers/ > > and specifically the following instructions: > > > > > > ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort > > ... output of configure ... > > make all install > > ... output of build and installation ... > > > > The result is shown below. As can be seen it was unsuccessful. I'll > appreciate > > some guidance here as I am nearing the deadline for a project that is part > of > > my research for my PhD. > > > > Thanks in advance. > > > > steph@sjb-linux:/src/openmpi-1.4.3$ ./configure --prefix=/opt/openmpi-1.4.3 > > CC=icc CXX=icpc F77=ifort FC=ifort > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > : command not foundconfig/missing: line 3: > > : command not foundconfig/missing: line 5: > > : command not foundconfig/missing: line 9: > > : command not foundconfig/missing: line 14: > > : command not foundconfig/missing: line 19: > > : command not foundconfig/missing: line 24: > > : command not foundconfig/missing: line 29: > > /src/openmpi-1.4.3/config/missing: line 49: syntax error near unexpected > token > > `'n > > 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in > > configure: WARNING: `missing' script is too old or missing > > checking for a thread-safe mkdir -p... /bin/mkdir -p > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > checking how to create a ustar tar archive... gnutar > > > > > > > == Configuring Open MPI > > > > > > > *** Checking versions > > : integer expression expected 3 > > : integer expression expected 0 > > .4ecking Open MPI version... 1 > > checking Open MPI release date... Oct 05, 2010 > > checking Open MPI Subversion repository version... r23834 > > : integer expression expected 3 > > : integer expression expected 0 > > .4ecking Open Run-Time Environment version... 1 > > checking Open Run-Time Environment release date... Oct 05, 2010 > > checking Open Run-Time Environment Subversion repository version... r23834 > > : integer expression expected 3 > > : integer expression expected 0 > > .4ecking Open Portable Access Layer version... 1 > > checking Open Portable Access Layer release date... Oct 05, 2010 > > checking Open Portable Access Layer Subversion repository version... r23834 > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > : command not found > > > > *** Initialization, setup > > configure: builddir: /src/openmpi-1.4.3 > > configure: srcdir: /src/openmpi-1.4.3 > > configure: error: cannot run /bin/sh config/config.sub > > steph@sjb-linux:/src/openmpi-1.4.3$ make all install > > make: *** No rule to make target `all'. Stop. > > steph@sjb-linux:/src/openmpi-1.4.3$ make install > > make: *** No rule to make target `install'. Stop. > > steph@sjb-linux:/src/openmpi-1.4.3$ > > > > > > Regards > > > > Steph Bredenhann > > > > > > > > > > > > > > -- > > This message was sent by Adept Internet's webmail. > > http://www.adept.co.za/ > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > -- This message was sent by Adept Internet's webmail. http://www.adept.co.za/ ompi-output.tar.bz2 Description: application/bzip
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Ah, I see why your output is munged -- there's a bunch of ^M's in there. It looks like OMPI's configure script got mucked up somehow. Did you expand the tarball on a windows machine and copy it over to a Linux box, perchance? If so, try expanding it directly on your Linux machine. On May 3, 2011, at 2:15 PM, Steph Bredenhann wrote: > Thanks for the speedy reply. The required file with information is attached. > > I first thought I must send the file to openmpi again, sorry if that was > wrong. > > Thanks > > > -- > Steph Bredenhann Pr.Eng Pr.CPM > > > Quoting Jeff Squyres : > >> Your output appears jumbled. Can you send all the data listed here: >> >>http://www.open-mpi.org/community/help/ >> >> On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: >> >>> Dear Sir/Madam >>> >>> I want to build openmpi for use with INTEL compilers (version 11.1) on my >> Ubuntu >>> 10.10 x64 system. I am using the guidelines from >>> >> > http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-open-mpi-with-the-intel-compilers/ >>> and specifically the following instructions: >>> >>> >>> ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort >>> ... output of configure ... >>> make all install >>> ... output of build and installation ... >>> >>> The result is shown below. As can be seen it was unsuccessful. I'll >> appreciate >>> some guidance here as I am nearing the deadline for a project that is part >> of >>> my research for my PhD. >>> >>> Thanks in advance. >>> >>> steph@sjb-linux:/src/openmpi-1.4.3$ ./configure --prefix=/opt/openmpi-1.4.3 >>> CC=icc CXX=icpc F77=ifort FC=ifort >>> checking for a BSD-compatible install... /usr/bin/install -c >>> checking whether build environment is sane... yes >>> : command not foundconfig/missing: line 3: >>> : command not foundconfig/missing: line 5: >>> : command not foundconfig/missing: line 9: >>> : command not foundconfig/missing: line 14: >>> : command not foundconfig/missing: line 19: >>> : command not foundconfig/missing: line 24: >>> : command not foundconfig/missing: line 29: >>> /src/openmpi-1.4.3/config/missing: line 49: syntax error near unexpected >> token >>> `'n >>> 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in >>> configure: WARNING: `missing' script is too old or missing >>> checking for a thread-safe mkdir -p... /bin/mkdir -p >>> checking for gawk... gawk >>> checking whether make sets $(MAKE)... yes >>> checking how to create a ustar tar archive... gnutar >>> >>> >> >>> == Configuring Open MPI >>> >> >>> >>> *** Checking versions >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open MPI version... 1 >>> checking Open MPI release date... Oct 05, 2010 >>> checking Open MPI Subversion repository version... r23834 >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open Run-Time Environment version... 1 >>> checking Open Run-Time Environment release date... Oct 05, 2010 >>> checking Open Run-Time Environment Subversion repository version... r23834 >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open Portable Access Layer version... 1 >>> checking Open Portable Access Layer release date... Oct 05, 2010 >>> checking Open Portable Access Layer Subversion repository version... r23834 >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> >>> *** Initialization, setup >>> configure: builddir: /src/openmpi-1.4.3 >>> configure: srcdir: /src/openmpi-1.4.3 >>> configure: error: cannot run /bin/sh config/config.sub >>> steph@sjb-linux:/src/openmpi-1.4.3$ make all install >>> make: *** No rule to make target `all'. Stop. >>> steph@sjb-linux:/src/openmpi-1.4.3$ make install >>> make: *** No rule to make target `install'. Stop. >>> steph@sjb-linux:/src/openmpi-1.4.3$ >>> >>> >>> Regards >>> >>> Steph Bredenhann >>> >>> >>> >>> >>> >>> >>> -- >>> This message was sent by Adept Internet's webmail. >>> http://www.adept.co.za/ >>> >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> -- >> Jeff Squyres >> jsquy...@cisco.com >> For corporate legal information go to: >> http://www.cisco.com/web/about/doing_business/legal/cri/ >> >> >> _
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
I think you are a genius! The new result is attached, it was only the last step make install that looked suspect. I'll appreciate if you can look at these results? While I am at it, thank you a million times for making this available to the public! Without openmpi I would not have been able to complete my PhD!!! Thanks -Original Message- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff Squyres Sent: Tuesday, May 03, 2011 21:27 To: Open MPI Users Subject: Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1 Ah, I see why your output is munged -- there's a bunch of ^M's in there. It looks like OMPI's configure script got mucked up somehow. Did you expand the tarball on a windows machine and copy it over to a Linux box, perchance? If so, try expanding it directly on your Linux machine. On May 3, 2011, at 2:15 PM, Steph Bredenhann wrote: > Thanks for the speedy reply. The required file with information is attached. > > I first thought I must send the file to openmpi again, sorry if that was wrong. > > Thanks > > > -- > Steph Bredenhann Pr.Eng Pr.CPM > > > Quoting Jeff Squyres : > >> Your output appears jumbled. Can you send all the data listed here: >> >>http://www.open-mpi.org/community/help/ >> >> On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: >> >>> Dear Sir/Madam >>> >>> I want to build openmpi for use with INTEL compilers (version 11.1) >>> on my >> Ubuntu >>> 10.10 x64 system. I am using the guidelines from >>> >> > http://software.intel.com/en-us/articles/performance-tools-for-softwar > e-developers-building-open-mpi-with-the-intel-compilers/ >>> and specifically the following instructions: >>> >>> >>> ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort >>> ... output of configure ... >>> make all install >>> ... output of build and installation ... >>> >>> The result is shown below. As can be seen it was unsuccessful. I'll >> appreciate >>> some guidance here as I am nearing the deadline for a project that >>> is part >> of >>> my research for my PhD. >>> >>> Thanks in advance. >>> >>> steph@sjb-linux:/src/openmpi-1.4.3$ ./configure >>> --prefix=/opt/openmpi-1.4.3 CC=icc CXX=icpc F77=ifort FC=ifort >>> checking for a BSD-compatible install... /usr/bin/install -c >>> checking whether build environment is sane... yes >>> : command not foundconfig/missing: line 3: >>> : command not foundconfig/missing: line 5: >>> : command not foundconfig/missing: line 9: >>> : command not foundconfig/missing: line 14: >>> : command not foundconfig/missing: line 19: >>> : command not foundconfig/missing: line 24: >>> : command not foundconfig/missing: line 29: >>> /src/openmpi-1.4.3/config/missing: line 49: syntax error near >>> unexpected >> token >>> `'n >>> 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in >>> configure: WARNING: `missing' script is too old or missing checking >>> for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... >>> gawk checking whether make sets $(MAKE)... yes checking how to >>> create a ustar tar archive... gnutar >>> >>> >> = >> === >>> == Configuring Open MPI >>> >> = >> === >>> >>> *** Checking versions >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open MPI version... 1 >>> checking Open MPI release date... Oct 05, 2010 checking Open MPI >>> Subversion repository version... r23834 >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open Run-Time Environment version... 1 checking Open >>> Run-Time Environment release date... Oct 05, 2010 checking Open >>> Run-Time Environment Subversion repository version... r23834 >>> : integer expression expected 3 >>> : integer expression expected 0 >>> .4ecking Open Portable Access Layer version... 1 checking Open >>> Portable Access Layer release date... Oct 05, 2010 checking Open >>> Portable Access Layer Subversion repository version... r23834 >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> : command not found >>> >>> *** Initialization, setup >>> configure: builddir: /src/openmpi-1.4.3 >>> configure: srcdir: /src/openmpi-1.4.3 >>> configure: error: cannot run /bin/sh config/config.sub >>> steph@sjb-linux:/src/openmpi-1.4.3$ make all install >>> make: *** No rule to make target `all'. Stop. >>> steph@sjb-linux:/src/openmpi-1.4.3$ make install >>> make: *** No rule to
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
That last error is because you don't have permission to install to /opt as a regular user. You need to run that command as "sudo make install". Damien On 03/05/2011 1:55 PM, Steph Bredenhann wrote: I think you are a genius! The new result is attached, it was only the last step make install that looked suspect. I'll appreciate if you can look at these results? While I am at it, thank you a million times for making this available to the public! Without openmpi I would not have been able to complete my PhD!!! Thanks -Original Message- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff Squyres Sent: Tuesday, May 03, 2011 21:27 To: Open MPI Users Subject: Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1 Ah, I see why your output is munged -- there's a bunch of ^M's in there. It looks like OMPI's configure script got mucked up somehow. Did you expand the tarball on a windows machine and copy it over to a Linux box, perchance? If so, try expanding it directly on your Linux machine. On May 3, 2011, at 2:15 PM, Steph Bredenhann wrote: Thanks for the speedy reply. The required file with information is attached. I first thought I must send the file to openmpi again, sorry if that was wrong. Thanks -- Steph Bredenhann Pr.Eng Pr.CPM Quoting Jeff Squyres: Your output appears jumbled. Can you send all the data listed here: http://www.open-mpi.org/community/help/ On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: Dear Sir/Madam I want to build openmpi for use with INTEL compilers (version 11.1) on my Ubuntu 10.10 x64 system. I am using the guidelines from http://software.intel.com/en-us/articles/performance-tools-for-softwar e-developers-building-open-mpi-with-the-intel-compilers/ and specifically the following instructions: ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort ... output of configure ... make all install ... output of build and installation ... The result is shown below. As can be seen it was unsuccessful. I'll appreciate some guidance here as I am nearing the deadline for a project that is part of my research for my PhD. Thanks in advance. steph@sjb-linux:/src/openmpi-1.4.3$ ./configure --prefix=/opt/openmpi-1.4.3 CC=icc CXX=icpc F77=ifort FC=ifort checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes : command not foundconfig/missing: line 3: : command not foundconfig/missing: line 5: : command not foundconfig/missing: line 9: : command not foundconfig/missing: line 14: : command not foundconfig/missing: line 19: : command not foundconfig/missing: line 24: : command not foundconfig/missing: line 29: /src/openmpi-1.4.3/config/missing: line 49: syntax error near unexpected token `'n 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar = === == Configuring Open MPI = === *** Checking versions : integer expression expected 3 : integer expression expected 0 .4ecking Open MPI version... 1 checking Open MPI release date... Oct 05, 2010 checking Open MPI Subversion repository version... r23834 : integer expression expected 3 : integer expression expected 0 .4ecking Open Run-Time Environment version... 1 checking Open Run-Time Environment release date... Oct 05, 2010 checking Open Run-Time Environment Subversion repository version... r23834 : integer expression expected 3 : integer expression expected 0 .4ecking Open Portable Access Layer version... 1 checking Open Portable Access Layer release date... Oct 05, 2010 checking Open Portable Access Layer Subversion repository version... r23834 : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found : command not found *** Initialization, setup configure: builddir: /src/openmpi-1.4.3 configure: srcdir: /src/openmpi-1.4.3 configure: error: cannot run /bin/sh config/config.sub steph@sjb-linux:/src/openmpi-1.4.3$ make all install make: *** No rule to make target `all'. Stop. steph@sjb-linux:/src/openmpi-1.4.3$ make install make: *** No rule to make target `install'. Stop. steph@sjb-linux:/src/openmpi-1.4.3$ Regards Steph Bredenhann -- This message was sent by Adept Internet's webmail. http://www.adept.co.za/ ___ users
Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1
Done, thanks a lot, the result is attached again for final scrutiny. And I have now moved to my Linux box so as NOT to make a mistake with Windows again! Regards Steph On Tue, 2011-05-03 at 13:59 -0600, Damien wrote: > That last error is because you don't have permission to install > to /opt as a regular user. You need to run that command as "sudo > make install". > > Damien > > On 03/05/2011 1:55 PM, Steph Bredenhann wrote: > > > I think you are a genius! > > > > The new result is attached, it was only the last step make install that > > looked suspect. > > > > I'll appreciate if you can look at these results? > > > > While I am at it, thank you a million times for making this available to the > > public! Without openmpi I would not have been able to complete my PhD!!! > > > > Thanks > > > > -Original Message- > > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > > Behalf Of Jeff Squyres > > Sent: Tuesday, May 03, 2011 21:27 > > To: Open MPI Users > > Subject: Re: [OMPI users] BUILDING OPENMPI ON UBUNTU WITH INTEL 11.1 > > > > Ah, I see why your output is munged -- there's a bunch of ^M's in there. > > > > It looks like OMPI's configure script got mucked up somehow. Did you expand > > the tarball on a windows machine and copy it over to a Linux box, perchance? > > If so, try expanding it directly on your Linux machine. > > > > > > > > On May 3, 2011, at 2:15 PM, Steph Bredenhann wrote: > > > > > > > Thanks for the speedy reply. The required file with information is > > > > attached. > > > > > I first thought I must send the file to openmpi again, sorry if that was > > > > wrong. > > > > > Thanks > > > > > > > > > -- > > > Steph Bredenhann Pr.Eng Pr.CPM > > > > > > > > > Quoting Jeff Squyres : > > > > > > > > > > Your output appears jumbled. Can you send all the data listed here: > > > > > > > >http://www.open-mpi.org/community/help/ > > > > > > > > On May 3, 2011, at 1:36 PM, Steph Bredenhann wrote: > > > > > > > > > > > > > Dear Sir/Madam > > > > > > > > > > I want to build openmpi for use with INTEL compilers (version 11.1) > > > > > on my > > > > > > > > Ubuntu > > > > > > > > > 10.10 x64 system. I am using the guidelines from > > > > > > > > > > > http://software.intel.com/en-us/articles/performance-tools-for-softwar > > > e-developers-building-open-mpi-with-the-intel-compilers/ > > > > > > > > and specifically the following instructions: > > > > > > > > > > > > > > > ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort > > > > > ... output of configure ... > > > > > make all install > > > > > ... output of build and installation ... > > > > > > > > > > The result is shown below. As can be seen it was unsuccessful. I'll > > > > > > > > appreciate > > > > > > > > > some guidance here as I am nearing the deadline for a project that > > > > > is part > > > > > > > > of > > > > > > > > > my research for my PhD. > > > > > > > > > > Thanks in advance. > > > > > > > > > > steph@sjb-linux:/src/openmpi-1.4.3$ ./configure > > > > > --prefix=/opt/openmpi-1.4.3 CC=icc CXX=icpc F77=ifort FC=ifort > > > > > checking for a BSD-compatible install... /usr/bin/install -c > > > > > checking whether build environment is sane... yes > > > > > : command not foundconfig/missing: line 3: > > > > > : command not foundconfig/missing: line 5: > > > > > : command not foundconfig/missing: line 9: > > > > > : command not foundconfig/missing: line 14: > > > > > : command not foundconfig/missing: line 19: > > > > > : command not foundconfig/missing: line 24: > > > > > : command not foundconfig/missing: line 29: > > > > > /src/openmpi-1.4.3/config/missing: line 49: syntax error near > > > > > unexpected > > > > > > > > token > > > > > > > > > `'n > > > > > 'src/openmpi-1.4.3/config/missing: line 49: `case $1 in > > > > > configure: WARNING: `missing' script is too old or missing checking > > > > > for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... > > > > > gawk checking whether make sets $(MAKE)... yes checking how to > > > > > create a ustar tar archive... gnutar > > > > > > > > > > > > > > > > > > = > > > > === > > > > > > > > > == Configuring Open MPI > > > > > > > > > > > > > = > > > > === > > > > > > > > > *** Checking versions > > > > > : integer expression expected 3 > > > > > : integer expression expected 0 > > > > > .4ecking Open MPI version... 1 > > > > > checking Open MPI release date... Oct 05, 2010 checking Open MPI > > > > > Subversion repository version... r23834 > > > > > : integer expression expected 3 > > > > > : integer expression expected 0 > > > > > .4ecking Open Run-Time Environment version... 1 checking Open > > > > > Run-Time Environment release date... Oct 05, 2010 checking Open > > > > > Run-Time Environment Subversion repo
[OMPI users] Open MPI 1.4.3 - Mac OS X 10.6.7
Hello: I am trying to install OpenMPI 1.4.3 on a Mac OS 10.6.7. I have installed Gfortran GCC 4.4.4 and Absoft11.0. It appears that I have i686-apple-darwin10-gcc-4.2.1. When I run ./configure --prefix=/opt/openmpi1.4.3 F77=/Applications/Absoft11.0/bin/f77 and ./configure --prefix=/opt/openmpi1.4.3GF F77=/sw/bin/gfortran in both cases I get the message: == It appears that your Fortran 77 compiler is unable to link against object files created by your C compiler. This typically indicates one of a few possibilities: - A conflict between CFLAGS and FFLAGS - A problem with your compiler installation(s) - Different default build options between compilers (e.g., C building for 32 bit and Fortran building for 64 bit) - Incompatible compilers Such problems can usually be solved by picking compatible compilers and/or CFLAGS and FFLAGS. More information (including exactly what command was given to the compilers and what error resulted when the commands were executed) is available in the config.log file in this directory. ** configure: error: C and Fortran 77 compilers are not link compatible. Can not continue. == I read the FAQ but did not find suggestions about this problem. What should be my next step? Thank you, Paul
Re: [OMPI users] Building openmpi with PGI 11.4: won't find torque??
My gzipp'ed config.log is attached. Thanks! --Jim On Tue, May 3, 2011 at 4:52 AM, Jeff Squyres wrote: > It should search both tmdir/lib and tmdir/lib64 by default, IIRC. > > Please send your config.log (please compress); it'll contain the specific > reason why configure didn't find libtorque. > > > On May 2, 2011, at 10:21 PM, Ralph Castain wrote: > >> It's probably looking for the torque lib in lib instead of lib64. There >> should be a configure option to tell it --with-tm-libdir or something like >> that - check "configure -h" >> >> >> On May 2, 2011, at 6:22 PM, Jim Kusznir wrote: >> >>> Hi all: >>> >>> I'm trying to build openmpi 1.4.3 against PGI 11.4 on my Rocks 5.1 >>> system. My "tried and true" build command for OpenMPI is: >>> >>> CC=pgcc CXX=pgCC F77=pgf77 FC=pgf90 rpmbuild -bb --define >>> 'install_in_opt 1' --define 'install_modulefile 1' --define >>> 'modules_rpm_name environment-modules' --define 'build_all_in_one_rpm >>> 0' --define 'configure_options --with-tm=/opt/torque' --define '_name >>> openmpi-pgi2011' --define 'use_default_rpm_opt_flags 0' >>> openmpi-1.4.3.spec >>> >>> This is what I've used to build openmpi 1.4.3 for gcc and against PGI >>> 8.x (our last version of PGI installed). This time, its not working, >>> though, and with what I consider to be a very strange failure point: >>> >>> --- MCA component plm:tm (m4 configuration macro) >>> checking for MCA component plm:tm compile mode... dso >>> checking --with-tm value... sanity check ok (/opt/torque) >>> checking for pbs-config... /opt/torque/bin/pbs-config >>> checking tm.h usability... yes >>> checking tm.h presence... yes >>> checking for tm.h... yes >>> checking for tm_finalize... no >>> checking tm.h usability... yes >>> checking tm.h presence... yes >>> checking for tm.h... yes >>> looking for library in lib >>> checking for tm_init in -lpbs... no >>> looking for library in lib64 >>> checking for tm_init in -lpbs... no >>> looking for library in lib >>> checking for tm_init in -ltorque... no >>> looking for library in lib64 >>> checking for tm_init in -ltorque... no >>> configure: error: TM support requested but not found. Aborting >>> error: Bad exit status from /var/tmp/rpm-tmp.7564 (%build) >>> >>> >>> However, /opt/torque/ is present. /opt/torque/bin/pbs-config returns: >>> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --prefix >>> /opt/torque >>> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --package >>> pbs >>> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --version >>> 2.3.0 >>> [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --libs >>> -L/opt/torque/lib64 -ltorque -Wl,--rpath -Wl,/opt/torque/lib64 >>> >>> and /opt/torque/lib64 does have: >>> [root@aeolus modulefiles]# ls /opt/torque/lib64 >>> libtorque.a libtorque.la libtorque.so libtorque.so.2 libtorque.so.2.0.0 >>> >>> so I'm a bit dumbfounded as to why configure doesn't "find" torque >>> support...Any suggestions? >>> >>> --Jim >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > config.log.gz Description: GNU Zip compressed data
Re: [OMPI users] Building openmpi with PGI 11.4: won't find torque??
Here's the issue: configure:110046: checking for tm_finalize configure:110102: pgcc -o conftest -O -DNDEBUG-D_REENTRANT -I/opt/torque/include-L/opt/torque/lib64 -Wl,--rpath -Wl,/opt/torque/lib64 conftest.c -lnsl -lutil-ltorque >&5 /usr/bin/ld: skipping incompatible /opt/torque/lib64/libtorque.so when searching for -ltorque /usr/bin/ld: skipping incompatible /opt/torque/lib64/libtorque.a when searching for -ltorque /usr/bin/ld: cannot find -ltorque Somehow the compiler/linker doesn't think that /opt/torque/lib64/libtorque.so is compatible. Is pgcc making 32 bit executables by default? I.e., do you need to specify some flag to pgcc to force it to make 64 bit executables? If so, specify it in CFLAGS --- something like this: ./configure CC=pgcc CXX=pgCC FC=pgfortran F77=pgfortran CFLAGS=-m64 \ CXXFLAGS=-m64 FCFLAGS=-m64 FFLAGS=-m64 ... (I don't know that it's -m64; I just made that out) On May 3, 2011, at 6:21 PM, Jim Kusznir wrote: > My gzipp'ed config.log is attached. Thanks! > --Jim > > On Tue, May 3, 2011 at 4:52 AM, Jeff Squyres wrote: >> It should search both tmdir/lib and tmdir/lib64 by default, IIRC. >> >> Please send your config.log (please compress); it'll contain the specific >> reason why configure didn't find libtorque. >> >> >> On May 2, 2011, at 10:21 PM, Ralph Castain wrote: >> >>> It's probably looking for the torque lib in lib instead of lib64. There >>> should be a configure option to tell it --with-tm-libdir or something like >>> that - check "configure -h" >>> >>> >>> On May 2, 2011, at 6:22 PM, Jim Kusznir wrote: >>> Hi all: I'm trying to build openmpi 1.4.3 against PGI 11.4 on my Rocks 5.1 system. My "tried and true" build command for OpenMPI is: CC=pgcc CXX=pgCC F77=pgf77 FC=pgf90 rpmbuild -bb --define 'install_in_opt 1' --define 'install_modulefile 1' --define 'modules_rpm_name environment-modules' --define 'build_all_in_one_rpm 0' --define 'configure_options --with-tm=/opt/torque' --define '_name openmpi-pgi2011' --define 'use_default_rpm_opt_flags 0' openmpi-1.4.3.spec This is what I've used to build openmpi 1.4.3 for gcc and against PGI 8.x (our last version of PGI installed). This time, its not working, though, and with what I consider to be a very strange failure point: --- MCA component plm:tm (m4 configuration macro) checking for MCA component plm:tm compile mode... dso checking --with-tm value... sanity check ok (/opt/torque) checking for pbs-config... /opt/torque/bin/pbs-config checking tm.h usability... yes checking tm.h presence... yes checking for tm.h... yes checking for tm_finalize... no checking tm.h usability... yes checking tm.h presence... yes checking for tm.h... yes looking for library in lib checking for tm_init in -lpbs... no looking for library in lib64 checking for tm_init in -lpbs... no looking for library in lib checking for tm_init in -ltorque... no looking for library in lib64 checking for tm_init in -ltorque... no configure: error: TM support requested but not found. Aborting error: Bad exit status from /var/tmp/rpm-tmp.7564 (%build) However, /opt/torque/ is present. /opt/torque/bin/pbs-config returns: [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --prefix /opt/torque [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --package pbs [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --version 2.3.0 [root@aeolus modulefiles]# /opt/torque/bin/pbs-config --libs -L/opt/torque/lib64 -ltorque -Wl,--rpath -Wl,/opt/torque/lib64 and /opt/torque/lib64 does have: [root@aeolus modulefiles]# ls /opt/torque/lib64 libtorque.a libtorque.la libtorque.so libtorque.so.2 libtorque.so.2.0.0 so I'm a bit dumbfounded as to why configure doesn't "find" torque support...Any suggestions? --Jim ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> -- >> Jeff Squyres >> jsquy...@cisco.com >> For corporate legal information go to: >> http://www.cisco.com/web/about/doing_business/legal/cri/ >> >> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] Open MPI 1.4.3 - Mac OS X 10.6.7
On May 3, 2011, at 5:29 PM, Paul Cizmas wrote: > I have installed Gfortran GCC 4.4.4 and Absoft11.0. > > It appears that I have i686-apple-darwin10-gcc-4.2.1. > > When I run > > ./configure --prefix=/opt/openmpi1.4.3 F77=/Applications/Absoft11.0/bin/f77 > > and > > ./configure --prefix=/opt/openmpi1.4.3GF F77=/sw/bin/gfortran > > in both cases I get the message: > > == > It appears that your Fortran 77 compiler is unable to link against > object files created by your C compiler. This typically indicates > one of a few possibilities: > > - A conflict between CFLAGS and FFLAGS > - A problem with your compiler installation(s) > - Different default build options between compilers (e.g., C >building for 32 bit and Fortran building for 64 bit) > - Incompatible compilers The problem is exactly what Open MPI is telling you -- the C compiler is not compatible with the Fortran compilers that you have specified. If you have /sw/bin/gfortran, I'm guessing you have it installed via fink...? If so, you might also have a fink-installed gcc that is compatible with that gfortran. -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] is there an equiv of iprove for bcast?
I don't quite understand your architecture enough to answer your question. E.g., someone pointed out to me off-list that if you only have 1 listener, a send is effectively the same thing as a broadcast (for which you could test/wait on a non-blocking receive, for example). MPI broadcasts only work on fixed communicators -- meaning that you effectively have to know the root and the receivers ahead of time. If the receivers don't know who the root will be beforehand, that's unfortunately not a good match for the MPI_Bcast operation. On May 3, 2011, at 4:07 AM, Randolph Pullen wrote: > > From: Randolph Pullen > Subject: Re: Re: [OMPI users] is there an equiv of iprove for bcast? > To: us...@open-mpi.or > Received: Monday, 2 May, 2011, 12:53 PM > > Non blocking Bcasts or tests would do it. > I currently have the clearing-house solution working but it is unsatisfying > because of its serial node. - As it scales it will overload this node. > > The problem rephrased: > Instead of n*2 processes, I am having to use n*2+1 with the extra process > serially receiving listener messages on behalf of the workers before > transmitting these messages to workers in its comm_group. > > Is there a way to Bcast directly from each listener to the worker pool? > (listeners must monitor their ports most of the time and cant participate in > global bcasts) > Not knowing which listener is going to transmit prevents the correct > comm_group being used with Bcast calls. > > --- On Sat, 30/4/11, Jeff Squyres wrote: > > From: Jeff Squyres > Subject: Re: [OMPI users] is there an equiv of iprove for bcast? > To: randolph_pul...@yahoo.com.au, "Open MPI Users" > Received: Saturday, 30 April, 2011, 7:17 AM > > On Apr 29, 2011, at 1:21 AM, Randolph Pullen wrote: > > > I am having a design issue: > > My server application has 2 processes per node, 1 listener and 1 worker. > > Each listener monitors a specified port for incoming TCP connections with > > the goal that on receipt of a request it will distribute it over the > > workers in a SIMD fashion. > > > > My problem is this: how can I get the workers to accept work from any of > > the listeners? > > Making a separate communicator does not help as the sender is unknown. > > Other than making a serial 'clearing house' process I cant think of a way > > - Iprobe for Bcast would be useful. > > I'm not quite sure I understand your question. > > There currently is no probe for collectives, but MPI-3 has non-blocking > collectives which you could MPI_Test for. There's a 3rd party library > implementation called libNBC (non-blocking collectives) that you could use > until such things become natively available. > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] [Wrf-users] WRF Problem running in Parallel on multiple nodes(cluster)
Dear Bart, I think OpenMPI don't need to be installed on all machines because they are NFS shared with the master node. I don't know how to check output of which orted, it is running just on the master node. I have another application which is running similarly but I am having problem with WRF. On Tue, May 3, 2011 at 9:06 PM, Bart Brashers wrote: > It looks like OpenMPI is not installed on all your execution machines. You > need to install at least the libs on all machines, or on an NFS-shared > location. Check the output of "which orted" on the machine that works. > > > > Bart > > > > *From:* wrf-users-boun...@ucar.edu [mailto:wrf-users-boun...@ucar.edu] *On > Behalf Of *Ahsan Ali > *Sent:* Tuesday, May 03, 2011 1:04 AM > *To:* us...@open-mpi.org > *Subject:* [Wrf-users] WRF Problem running in Parallel on multiple > nodes(cluster) > > > > Hello, > > > > I am able to run WRFV3.2.1 using mpirun on multiple cores of single > machine, but when I want to run it across multiple nodes in cluster using > hostlist then I get error, The compute nodes are mounted with the master > node during boot using NFS. I get following error. Please help. > > > > [root@pmd02 em_real]# mpirun -np 10 -hostfile /home/pmdtest/hostlist > ./real.exe > > bash: orted: command not found > > bash: orted: command not found > > -- > > A daemon (pid 22006) died unexpectedly with status 127 while attempting > > to launch so we are aborting. > > > > There may be more information reported by the environment (see above). > > > > This may be because the daemon was unable to find all the needed shared > > libraries on the remote node. You may set your LD_LIBRARY_PATH to have the > > location of the shared libraries on the remote nodes and this will > > automatically be forwarded to the remote nodes. > > -- > > -- > > mpirun noticed that the job aborted, but has no info as to the process > > that caused that situation. > > -- > > mpirun: clean termination accomplished > > > > > -- > Syed Ahsan Ali Bokhari > Electronic Engineer (EE) > > > Research & Development Division > Pakistan Meteorological Department H-8/4, Islamabad. > Phone # off +92518358714 > > Cell # +923155145014 > > > > -- > This message contains information that may be confidential, privileged or > otherwise protected by law from disclosure. It is intended for the exclusive > use of the Addressee(s). Unless you are the addressee or authorized agent of > the addressee, you may not review, copy, distribute or disclose to anyone > the message or any information contained within. If you have received this > message in error, please contact the sender by electronic reply to > em...@environcorp.com and immediately delete all copies of the message. > > -- Syed Ahsan Ali Bokhari Electronic Engineer (EE) Research & Development Division Pakistan Meteorological Department H-8/4, Islamabad. Phone # off +92518358714 Cell # +923155145014
Re: [OMPI users] is there an equiv of iprove for bcast?
Sorry, I meant to say:- on each node there is 1 listener and 1 worker.- all workers act together when any of the listeners send them a request.- currently I must use an extra clearinghouse process to receive from any of the listeners and bcast to workers, this is unfortunate because of the potential scaling issues I think you have answered this in that I must wait for MPI-3's non-blocking collectives. Can anyone suggest another way? I don't like the serial clearinghouse approach. --- On Wed, 4/5/11, Jeff Squyres wrote: From: Jeff Squyres Subject: Re: [OMPI users] is there an equiv of iprove for bcast? To: randolph_pul...@yahoo.com.au, "Open MPI Users" Received: Wednesday, 4 May, 2011, 11:19 AM I don't quite understand your architecture enough to answer your question. E.g., someone pointed out to me off-list that if you only have 1 listener, a send is effectively the same thing as a broadcast (for which you could test/wait on a non-blocking receive, for example). MPI broadcasts only work on fixed communicators -- meaning that you effectively have to know the root and the receivers ahead of time. If the receivers don't know who the root will be beforehand, that's unfortunately not a good match for the MPI_Bcast operation. On May 3, 2011, at 4:07 AM, Randolph Pullen wrote: > > From: Randolph Pullen > Subject: Re: Re: [OMPI users] is there an equiv of iprove for bcast? > To: us...@open-mpi.or > Received: Monday, 2 May, 2011, 12:53 PM > > Non blocking Bcasts or tests would do it. > I currently have the clearing-house solution working but it is unsatisfying > because of its serial node. - As it scales it will overload this node. > > The problem rephrased: > Instead of n*2 processes, I am having to use n*2+1 with the extra process > serially receiving listener messages on behalf of the workers before > transmitting these messages to workers in its comm_group. > > Is there a way to Bcast directly from each listener to the worker pool? > (listeners must monitor their ports most of the time and cant participate in > global bcasts) > Not knowing which listener is going to transmit prevents the correct > comm_group being used with Bcast calls. > > --- On Sat, 30/4/11, Jeff Squyres wrote: > > From: Jeff Squyres > Subject: Re: [OMPI users] is there an equiv of iprove for bcast? > To: randolph_pul...@yahoo.com.au, "Open MPI Users" > Received: Saturday, 30 April, 2011, 7:17 AM > > On Apr 29, 2011, at 1:21 AM, Randolph Pullen wrote: > > > I am having a design issue: > > My server application has 2 processes per node, 1 listener and 1 worker. > > Each listener monitors a specified port for incoming TCP connections with > > the goal that on receipt of a request it will distribute it over the > > workers in a SIMD fashion. > > > > My problem is this: how can I get the workers to accept work from any of > > the listeners? > > Making a separate communicator does not help as the sender is unknown. > > Other than making a serial 'clearing house' process I cant think of a way > > - Iprobe for Bcast would be useful. > > I'm not quite sure I understand your question. > > There currently is no probe for collectives, but MPI-3 has non-blocking > collectives which you could MPI_Test for. There's a 3rd party library > implementation called libNBC (non-blocking collectives) that you could use > until such things become natively available. > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
