[OMPI users] openmpi/numa

WChem 5.0) that is built-in parallelized with TCGMSG. Thanks francesco pietra Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC

[OMPI users] intel/openmpi

--This is a problem of the local compiler, not of openmpi. Attached is the config.log. Kind regards francesco pietra Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories

Re: [OMPI users] intel/openmpi

Sorry for the mistake "CXX=/opt/.icc" below. Actually the command was issued correctly, with "CXX=/ot/...icpc". I have checked that directly by searching back for issued commands. francesco pietra --- George Bosilca wrote: > I run into this few weeks ago. The

[OMPI users] Fwd: intel/openmpi

Sorry for the mistake "CXX=/opt/.icc" below. Actually the command was issued correctly, with "CXX=/ot/...icpc". I have checked that directly by searching back for issued commands. francesco pietra --- Francesco Pietra wrote: > Date: Sun, 24 Jun 2007 01:47:13 -0700

Re: [OMPI users] intel/openmpi

Henry: Thanks. The "icc" issue did not exist. The command line of ./configure was correct for CXX respect. What was wrong was the lack of "/bin" before icpc. Then, both ./configure and make commands OK. Then, I tried # checkinstall make install which aborted (checkinstall has been removed from

[OMPI users] Fwd: Re: intel/openmpi

that investigation to realize why the compilation of openmpi seems to be OK according to the test they suggest. regards francesco pietra --- Francesco Pietra wrote: > Date: Mon, 25 Jun 2007 09:12:27 -0700 (PDT) > From: Francesco Pietra > Subject: Re: [OMPI users] intel/openmpi > T

[OMPI users] MPI_HOME

location of the include/ and lib/ subdirectories containing mpi.f libmpi.a liblam.a liblamf77mpi.a which was confusing to me. None of these libraries on my system and I never advocated lam Thanks for helping francesco pietra

Re: [OMPI users] openmpi support ignored

I can't expect that the problem is studied on the openmpi site. Thanks francesco pietra --- Jeff Squyres wrote: > On Jul 23, 2007, at 5:11 PM, Bert Wesarg wrote: > > >> I'm not sure what these command line switches do...? "-openmpi" is > >> not a s

Re: [OMPI users] openmpi support ignored

case would be to adapt flags amber/openmpi in order that openmpi understands what amber is looking for. What you wrote probably could help to this regard. Thanks francesco pietra --- Andrey Kaliazin wrote: Hi all, I have compiled Amber9 with OpenMPI 1.2 without a hitch. Machine - an 8-way (16

[OMPI users] mpi daemon

hanks francesco pietra Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7

[OMPI users] Two different compilation of openmpi

y. I rule out the alternative of compiling Amber9 with GNU compilers, which will run slower. Thanks francesco pietra Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/

Re: [OMPI users] Open MPI v1.2.4 released

Are any detailed directions for upgrading (for common guys, not experts, I mean)? My 1.2.3 version on Debian Linux amd64 runs perfectly. Thanks francesco pietra --- Tim Mattox wrote: > The Open MPI Team, representing a consortium of research, academic, > and industry partners, is plea

[OMPI users] Segmentation fault

] [deb64:03540] *** End of error message *** mpirun noticed that jpb rank 0 with PID 3537 on node deb64 exited on signal 15 (Terminated). 3 additional processes aborted (not shown) Thanks francesco pietra __ Do You Yahoo!? Tired of spam? Yahoo! Mail

Re: [OMPI users] Segmentation fault

ing in terms of binary compatibility between versions. > > > On Nov 7, 2007, at 8:05 AM, Francesco Pietra wrote: > > > I wonder whether any suggestion can be offered about segmentation > > fault > > occurring on running a docking program (DOCK 6.1, written in C) on &g

Re: [OMPI users] Segmentation fault

--- Adrian Knoth wrote: > On Wed, Nov 07, 2007 at 08:09:14AM -0500, Jeff Squyres wrote: > > > I'm not familiar with DOCK or Debian, but you will definitely have > > And last but not least, Surely not last. My OpenMPI was intel compiled. Simple reason: Amber9, as a Fortran program, runs fast

Re: [OMPI users] Segmentation fault

On Wed, Nov 07, 2007 at 07:00:31 -0800, Francesco Pietra wrote: > I was lucky, given my modest skill with systems. In a couple of hours the system is OK again. DOCK, configured for MPICH and compiled gcc, is now running parallel with pointing to OpenMPI 1.2.3 compiled ifort/icc. Top -i shows

Re: [OMPI users] Open MPI v1.2.5 released

? (several instances in my system) What about programs that were compiled from config configured for mpich2, though run parallel by pointing to Open MPI 1.2 (one instance in my system). Thanks francesco pietra --- Tim Mattox wrote: > The Open MPI Team, representing a consortium of research, ac

[OMPI users] Replace 1.2.3 with 1.2.6

figures stand for me as user) from which I carried out the compilation. /usr/local/bin contains: mpic++ mpicc mpiCC mpicxx mpiexec mpif77 mpif90 mpirun ompi_info orted orterun are these overwritten during the new compilation, or some deletion is needed? Thanks francesco pietra If I understand, the

[OMPI users] installation with two different compilers

o `opal_progress_mpi_enable' make[3]: *** [octopus_mpi] Error 1 make[3]: Leaving directory `/home/francesco/octopus/octopus-3.1.0/src/main' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/francesco/octopus/octopus-3.1.0/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/francesco/octopus/octopus-3.1.0' make: *** [all] Error 2 francesco@tya64:~/octopus/octopus-3.1.0$ Thanks for help francesco pietra

[OMPI users] Fwd: installation with two different compilers

fo reports about previous installation of 1.2.6 version (intel). Is this situation correct for compiling a program with FC=/opt/bin/mpif90 CC=/opt/bin/mpicc etcetera ? How getting the runtime for the compiled program? I am asking all that because I have problems in the compilation, so tha

[OMPI users] support for gamess us?

supporting gamess us parallelization with openmpi, or any form of mpi as a seed to move to openmpi? thanks francesco pietra

[OMPI users] support for gamess us?

supporting gamess us parallelization with openmpi, or any form of mpi as a seed to move to openmpi? thanks francesco pietra

[OMPI users] Issues on install 1.3.1

compiler NO refers: gcc or intel? I would also appreciate very much a direction how to chech gcc and intel C++ independently. I checked that: which ifort /opt/intel/fce/10.1.015/bin/ifort in my .bashrc: . /opt/intel/fce/10.1.015/bin/ifortvars.sh (and iccvars.sh) thanks francesco pietra

Re: [OMPI users] Issues on install 1.3.1

Observatory - Columbia University > Palisades, NY, 10964-8000 - USA > ----- > > Jeff Squyres wrote: >> >> On Apr 2, 2009, at 7:21 AM, Francesco Pietra wrote: >> >>> Hi: >>> With debian linux amd64 lenny I tried to install openmpi-1.3.1 instead >>>

Re: [OMPI users] Issues on install 1.3.1

As far as I understand, apt-get install libnuma1 libnuma-dbg libnuma-dev installs libnuma libraries 64 bit in /usr/lib there also two symlinks /usr/lib32 and /usr/lib64 but there is no trace of the libnuma libraries there. That the computational codes I use run twice as fast at 64 bit than 32 bi

Re: [OMPI users] Issues on install 1.3.1

n? thanks francesco On Thu, Apr 2, 2009 at 1:46 PM, Jeff Squyres wrote: > On Apr 2, 2009, at 7:21 AM, Francesco Pietra wrote: > >> Hi: >> With debian linux amd64 lenny I tried to install openmpi-1.3.1 instead >> of using the executables openmpi-1.2.6 of previous disks. I c

[OMPI users] libnuma issue

/ifort --with-libnuma=/usr/lib failed because "expected file /usr/lib/include/numa.h was not found" In debian amd64 lenny numa.h has a different location "/usr/include/numa.h". Attached is the config.log. I would appreciate help in circumventing the problem. Thanks france

Re: [OMPI users] libnuma issue

I was not sure whether that is a technically correct procedure. It works. Thanks francesco On Fri, Apr 3, 2009 at 6:05 PM, John Hearns wrote: > 2009/4/3 Francesco Pietra : >> > "expected file /usr/lib/include/numa.h was not found" >> >> In debian amd64 len

Re: [OMPI users] libnuma issue

I'm interested in does not want to be compiled. Now, with the parallel support in order, I hope. francesco On Fri, Apr 3, 2009 at 7:04 PM, John Hearns wrote: > 2009/4/3 Francesco Pietra : >> I was not sure whether that is a technically correct procedure. It works. >> Tha

[OMPI users] ssh MPi and program tests

arose at the time of amd64 etch with the same configuration of ssh, same compilers, and openmpi 1.2.6. I am here because the warning from the amber site is that I should to learn how to use my installation of MPI. Therefore, if there is any clue .. thanks francesco pietra

Re: [OMPI users] ssh MPi and program tests

I hope this helps. > Gus Correa > - > Gustavo Correa > Lamont-Doherty Earth Observatory - Columbia University > Palisades, NY, 10964-8000 - USA > -

Re: [OMPI users] ssh MPi and program tests

Hi Francesco, list > > Francesco Pietra wrote: >> >> On Mon, Apr 6, 2009 at 5:21 PM, Gus Correa wrote: >>> >>> Hi Francesco >>> >>> Did you try to run examples/connectivity_c.c, >>> or examples/hello_c.c before trying amber? >>

Re: [OMPI users] ssh MPi and program tests

2009 at 11:03 PM, Gus Correa wrote: > Hi Francesco > > > See answers inline. > > Francesco Pietra wrote: >> >> Hi Gus: >> Partial quick answers below. I have reestablished the ssh connection >> so that tomorrow I'll run the tests. Everything t

Re: [OMPI users] ssh MPi and program tests

y don't > show up in `man mpirun`). > And i think you should add a "-n 4" (for 4 processors) > Furthermore, if you want to specify a host, you have to add "-host hostname1" > if you want to specify several hosts you have to add "-host > hostname1,hostnam

[OMPI users] Fwd: ssh MPi and program tests

3 of 4 Combine with all other investigations, the installation of openmpi 1.3.1 is correct. thanks a lot for your lesson francesco -- Forwarded message ------ From: Francesco Pietra List-Post: users@lists.open-mpi.org Date: Tue, Apr 7, 2009 at 11:39 AM Subject: Re: [OMPI users] ssh MPi a

[OMPI users] recompiling 1.3.1 with intels

intels 11 should I first do anything on openmpi which was compiled with intels 10? thanks francesco pietra

Re: [OMPI users] ssh MPi and program tests

print in what I wrote but at the moment i am unable to do better. All issues about ssh were resolved. Actually, there was no issue. I created the issues and apologize for that. thanks francesco On Wed, Apr 8, 2009 at 10:28 AM, Marco wrote: > * Francesco Pietra [2009 04 06, 16:51]: >> cd cy

Re: [OMPI users] recompiling 1.3.1 with intels

On Wed, Apr 8, 2009 at 12:59 PM, Jeff Squyres wrote: > On Apr 8, 2009, at 5:08 AM, Francesco Pietra wrote: > >> As I was unable to compile the parallel code Amber10 with openmpi >> 1.3.1 (fully tested) and intel compilers and mkl version 10 on debian >> amd64 lenny,

Re: [OMPI users] recompiling 1.3.1 with intels

ncesco > > I hope this helps. > Gus Correa > - > Gustavo Correa > Lamont-Doherty Earth Observatory - Columbia University > Palisades, NY, 10964-8000 - USA > -

[OMPI users] shared libraries issue compiling 1.3.1/intel 10.1.022

linking is highly recommended as opposed to setting LD_LIBRARY_PATH at run time, not the least because it hardcodes the paths to the "right" library files in the executables themselves" Should this be relevant to the present issue, where to learn about -rpath linking? thanks francesco pietra

Re: [OMPI users] shared libraries issue compiling 1.3.1/intel 10.1.022

t-dynamic -lnsl -lutil thanks francesco On Thu, Apr 9, 2009 at 9:29 PM, Gus Correa wrote: > Hi Francesco > > Francesco Pietra wrote: >> >> Hi: >> As failure to find "limits.h" in my attempted compilations of Amber of >> th fast few days (amd64 lenny,

[OMPI users] Fwd: shared libraries issue compiling 1.3.1/intel 10.1.022

Sorry, the first line of the ouput below (copied manually) should be rad /usr/local/bin/mpirun -host deb64 -n 4 connectivity_c 2>&1 | tee connectivity.ou -- Forwarded message -- From: Francesco Pietra List-Post: users@lists.open-mpi.org Date: Fri, Apr 10, 2009 at

Re: [OMPI users] Fwd: shared libraries issue compiling 1.3.1/intel 10.1.022

; Gus Correa > - > Gustavo Correa > Lamont-Doherty Earth Observatory - Columbia University > Palisades, NY, 10964-8000 - USA > - > > Francesco Pietra wr

Re: [OMPI users] shared libraries issue compiling 1.3.1/intel10.1.022

apply to the amber site because they have declined interest in adapting Amber9 to present software. Unfortunately I don't have two sufficiently powerful computers for present and vintage status. Thanks a lot for considering my mail francesco pietra On Fri, Apr 10, 2009 at 6:24 PM, Jeff Squyre

Re: [OMPI users] shared libraries issue compiling 1.3.1/intel 10.1.022

f you want to find libimf.so, which is a shared INTEL library, > pass the library path with a -x on mpirun > > mpirun -x LD_LIBRARY_PATH .... > > DM > > > On Fri, 10 Apr 2009, Francesco Pietra wrote: > >> Hi Gus: >> >> If you feel that the observations bel

Re: [OMPI users] libnuma issue

I used --with-libnuma=/usr since Prentice Bisbal's suggestion and it worked. Unfortunately, I found no way to fix the failure in finding libimf.so when compiling openmpi-1.3.1 with intels, as you have seen in other e-mail from me. And gnu compilers (which work well with both openmpi and the slower

Re: [OMPI users] libnuma issue

On Wed, Apr 15, 2009 at 8:39 PM, Prentice Bisbal wrote: > Francesco Pietra wrote: >> I used --with-libnuma=/usr since Prentice Bisbal's suggestion and it >> worked. Unfortunately, I found no way to fix the failure in finding >> libimf.so when compiling openmpi-1.3.1 wit

Re: [OMPI users] libnuma issue

rror: libimf.so not found (the library was sourced with the *.sh intel scripts) francesco On Thu, Apr 16, 2009 at 4:43 AM, Nysal Jan wrote: > You could try statically linking the Intel-provided libraries. Use > LDFLAGS=-static-intel > > --Nysal > > On Wed, 2009-04-15 at 21:03

Re: [OMPI users] Intel compiler libraries (was: libnuma issue)

n-interactively.  E.g.: > >  thisnode$ ssh othernode env | sort > > shows the relevant stuff in your environment on the other node.  Note that > this is different than > >  thisnode$ ssh othernode >  othernode$ env | sort > > > > > On Apr 16, 2009, at 8:56 AM

Re: [OMPI users] Intel compiler libraries (was: libnuma issue)

from the internal network. francesco On Thu, Apr 16, 2009 at 5:37 PM, Jeff Squyres wrote: > On Apr 16, 2009, at 11:29 AM, Francesco Pietra wrote: > >> francesco@tya64:~$ ssh 192.168.1.33 env | sort >> HOME=/home/francesco >> LANG=en_US.UTF-8 >> LOGNAME=francesco >&

Re: [OMPI users] Intel compiler libraries (was: libnuma issue)

On Thu, Apr 16, 2009 at 5:37 PM, Jeff Squyres wrote: > On Apr 16, 2009, at 11:29 AM, Francesco Pietra wrote: > >> francesco@tya64:~$ ssh 192.168.1.33 env | sort >> HOME=/home/francesco >> LANG=en_US.UTF-8 >> LOGNAME=francesco >> MAIL=/var/mail/francesco >&

Re: [OMPI users] Intel compiler libraries (was: libnuma issue)

On Thu, Apr 16, 2009 at 6:04 PM, Douglas Guptill wrote: > On Thu, Apr 16, 2009 at 05:29:14PM +0200, Francesco Pietra wrote: >> On Thu, Apr 16, 2009 at 3:04 PM, Jeff Squyres wrote: > ... >> Given my inexperience as system analyzer, I assume that I am messing >> somethi