[OMPI users] Help: HPL Problem
Hi, I encountered following error messages when I compiled HPL. make[2]: Entering directory `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' /pool/MPI/openmpi/bin/mpif90 -DAdd__ -DF77_INTEGER=int -DStringSunStyle -I/pool/measure/hpl-2.0/include -I/pool/measure/hpl-2.0/include/Linux_PII_FBLAS -I/pool/MPI/openmpi/include -fomit-frame-pointer -O3 -funroll-loops -W -Wall -o /pool/measure/hpl-2.0/bin/Linux_PII_FBLAS/xhpl HPL_pddriver.o HPL_pdinfo.o HPL_pdtest.o /pool/measure/hpl-2.0/lib/Linux_PII_FBLAS/libhpl.a /pool/libs/BLAS/blas_LINUX.a /pool/MPI/openmpi/lib/libmpi.so /usr/bin/ld: cannot find -ldl /usr/bin/ld: cannot find -lnsl /usr/bin/ld: cannot find -lutil /usr/bin/ld: cannot find -lm /usr/bin/ld: cannot find -ldl /usr/bin/ld: cannot find -lm collect2: ld returned 1 exit status make[2]: *** [dexe.grd] Error 1 make[2]: Leaving directory `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' make[1]: *** [build_tst] Error 2 make[1]: Leaving directory `/pool/measure/hpl-2.0' make: *** [build] Error 2 And the attachment is the make file I created. OS is Fedora 14 x86_64. Could anyone show me where is going wrong? Thanks. Eric Make.Linux_PII_FBLAS Description: Binary data
Re: [OMPI users] Help: HPL Problem
Eric, You have a link-time error complaining about the absence of some libraries. At least two of them libm and libdl must be provided by system, not by MPI implementation. Could you locate them in /usr/lib64? Also it should be useful to figure out if the problem is global or specific to HPL: do you have any errors compiling simple "hello world" program with OpenMPI? - D. 2011/5/7 Lee Eric : > Hi, > > I encountered following error messages when I compiled HPL. > > make[2]: Entering directory > `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' > /pool/MPI/openmpi/bin/mpif90 -DAdd__ -DF77_INTEGER=int > -DStringSunStyle -I/pool/measure/hpl-2.0/include > -I/pool/measure/hpl-2.0/include/Linux_PII_FBLAS > -I/pool/MPI/openmpi/include -fomit-frame-pointer -O3 -funroll-loops -W > -Wall -o /pool/measure/hpl-2.0/bin/Linux_PII_FBLAS/xhpl HPL_pddriver.o > HPL_pdinfo.o HPL_pdtest.o > /pool/measure/hpl-2.0/lib/Linux_PII_FBLAS/libhpl.a > /pool/libs/BLAS/blas_LINUX.a /pool/MPI/openmpi/lib/libmpi.so > /usr/bin/ld: cannot find -ldl > /usr/bin/ld: cannot find -lnsl > /usr/bin/ld: cannot find -lutil > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -ldl > /usr/bin/ld: cannot find -lm > collect2: ld returned 1 exit status > make[2]: *** [dexe.grd] Error 1 > make[2]: Leaving directory > `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' > make[1]: *** [build_tst] Error 2 > make[1]: Leaving directory `/pool/measure/hpl-2.0' > make: *** [build] Error 2 > > And the attachment is the make file I created. OS is Fedora 14 x86_64. > > Could anyone show me where is going wrong? Thanks. > > Eric > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] Help: HPL Problem
Hey mate, I have installed glibc-devel and it seems good. I also checked the status of the lib files they are all exist. Eric On Sat, May 7, 2011 at 11:11 PM, Dmitry N. Mikushin wrote: > Eric, > > You have a link-time error complaining about the absence of some > libraries. At least two of them libm and libdl must be provided by > system, not by MPI implementation. Could you locate them in > /usr/lib64? Also it should be useful to figure out if the problem is > global or specific to HPL: do you have any errors compiling simple > "hello world" program with OpenMPI? > > - D. > > 2011/5/7 Lee Eric : >> Hi, >> >> I encountered following error messages when I compiled HPL. >> >> make[2]: Entering directory >> `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' >> /pool/MPI/openmpi/bin/mpif90 -DAdd__ -DF77_INTEGER=int >> -DStringSunStyle -I/pool/measure/hpl-2.0/include >> -I/pool/measure/hpl-2.0/include/Linux_PII_FBLAS >> -I/pool/MPI/openmpi/include -fomit-frame-pointer -O3 -funroll-loops -W >> -Wall -o /pool/measure/hpl-2.0/bin/Linux_PII_FBLAS/xhpl HPL_pddriver.o >> HPL_pdinfo.o HPL_pdtest.o >> /pool/measure/hpl-2.0/lib/Linux_PII_FBLAS/libhpl.a >> /pool/libs/BLAS/blas_LINUX.a /pool/MPI/openmpi/lib/libmpi.so >> /usr/bin/ld: cannot find -ldl >> /usr/bin/ld: cannot find -lnsl >> /usr/bin/ld: cannot find -lutil >> /usr/bin/ld: cannot find -lm >> /usr/bin/ld: cannot find -ldl >> /usr/bin/ld: cannot find -lm >> collect2: ld returned 1 exit status >> make[2]: *** [dexe.grd] Error 1 >> make[2]: Leaving directory >> `/pool/measure/hpl-2.0/testing/ptest/Linux_PII_FBLAS' >> make[1]: *** [build_tst] Error 2 >> make[1]: Leaving directory `/pool/measure/hpl-2.0' >> make: *** [build] Error 2 >> >> And the attachment is the make file I created. OS is Fedora 14 x86_64. >> >> Could anyone show me where is going wrong? Thanks. >> >> Eric >> >> ___ >> 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 >
[OMPI users] USE mpi
I have compiled all my fortran source files successfully with openmpi 1.4.3 wrapper for ifort on Ubuntu 10.10, except the main progran file that contains the "include mpif.h" statement. It seems that the "include mpif.h" is deprecated and that one should now use "USE mpi". However, when compiling with this I get the following message: Compile... 3k-1.for(2): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [MPI] USE mpi --^ compilation aborted for 3k-1.for (code 1) done "/usr/include/mpi" is included in the variable $INCLUDE Could someone please advise on the next step to take? Thanks -- Steph Bredenhann
Re: [OMPI users] USE mpi
What is the compile line that you are using to compile your application? If you use "mpif90 ...", then the right compiler directive should be automatically added such that the mpi module will be found (assuming that your OMPI was installed with F90 support, that is). On May 7, 2011, at 2:09 PM, Steph Bredenhann wrote: > I have compiled all my fortran source files successfully with openmpi 1.4.3 > wrapper for ifort on Ubuntu 10.10, except the main progran file that contains > the "include mpif.h" statement. It seems that the "include mpif.h" is > deprecated and that one should now use "USE mpi". However, when compiling > with this I get the following message: > > Compile... > 3k-1.for(2): error #7002: Error in opening the compiled module file. Check > INCLUDE paths. [MPI] > USE mpi > --^ > compilation aborted for 3k-1.for (code 1) > done > > "/usr/include/mpi" is included in the variable $INCLUDE > > Could someone please advise on the next step to take? > > Thanks > > > > -- > Steph Bredenhann > > ___ > 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] USE mpi
Thanks for the quick feedback. My compile line is: /usr/bin/mpif90 -vec-report0 -O3 -r8 -assume byterecl $FILENAME -c I have built OMPI with IFORT. Regards --- Steph Bredenhann On Sat, 2011-05-07 at 14:26 -0400, Jeff Squyres wrote: > What is the compile line that you are using to compile your application? > > If you use "mpif90 ...", then the right compiler directive should be > automatically added such that the mpi module will be found (assuming that > your OMPI was installed with F90 support, that is). > > > On May 7, 2011, at 2:09 PM, Steph Bredenhann wrote: > > > I have compiled all my fortran source files successfully with openmpi 1.4.3 > > wrapper for ifort on Ubuntu 10.10, except the main progran file that > > contains the "include mpif.h" statement. It seems that the "include mpif.h" > > is deprecated and that one should now use "USE mpi". However, when > > compiling with this I get the following message: > > > > Compile... > > 3k-1.for(2): error #7002: Error in opening the compiled module file. Check > > INCLUDE paths. [MPI] > > USE mpi > > --^ > > compilation aborted for 3k-1.for (code 1) > > done > > > > "/usr/include/mpi" is included in the variable $INCLUDE > > > > Could someone please advise on the next step to take? > > > > Thanks > > > > > > > > -- > > Steph Bredenhann > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > >
Re: [OMPI users] USE mpi
What is the output of /usr/bin/mpif90 -vec-report0 -O3 -r8 -assume byterecl $FILENAME -c --showme And ompi_info | grep 90 On May 7, 2011, at 2:40 PM, Steph Bredenhann wrote: > Thanks for the quick feedback. > > My compile line is: > > /usr/bin/mpif90 -vec-report0 -O3 -r8 -assume byterecl $FILENAME -c > > I have built OMPI with IFORT. > > Regards > > --- > Steph Bredenhann > > On Sat, 2011-05-07 at 14:26 -0400, Jeff Squyres wrote: >> What is the compile line that you are using to compile your application? >> >> If you use "mpif90 ...", then the right compiler directive should be >> automatically added such that the mpi module will be found (assuming that >> your OMPI was installed with F90 support, that is). >> >> >> On May 7, 2011, at 2:09 PM, Steph Bredenhann wrote: >> >> > I have compiled all my fortran source files successfully with openmpi >> > 1.4.3 wrapper for ifort on Ubuntu 10.10, except the main progran file that >> > contains the "include mpif.h" statement. It seems that the "include >> > mpif.h" is deprecated and that one should now use "USE mpi". However, when >> > compiling with this I get the following message: >> > >> > Compile... >> > 3k-1.for(2): error #7002: Error in opening the compiled module file. >> > Check INCLUDE paths. [MPI] >> > USE mpi >> > --^ >> > compilation aborted for 3k-1.for (code 1) >> > done >> > >> > "/usr/include/mpi" is included in the variable $INCLUDE >> > >> > Could someone please advise on the next step to take? >> > >> > Thanks >> > >> > >> > >> > -- >> > Steph Bredenhann >> > >> > ___ >> > 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] USE mpi
The output is: ifort -I/opt/openmpi-1.4.3/include -pthread -I/opt/openmpi-1.4.3/lib -vec-report0 -O3 -r8 -assume byterecl 3k-1.for -c done --- Steph Bredenhann On Sat, 2011-05-07 at 14:46 -0400, Jeff Squyres wrote: > What is the output of > > /usr/bin/mpif90 -vec-report0 -O3 -r8 -assume byterecl $FILENAME -c --showme > > And > > ompi_info | grep 90 > > > > On May 7, 2011, at 2:40 PM, Steph Bredenhann wrote: > > > Thanks for the quick feedback. > > > > My compile line is: > > > > /usr/bin/mpif90 -vec-report0 -O3 -r8 -assume byterecl $FILENAME -c > > > > I have built OMPI with IFORT. > > > > Regards > > > > --- > > Steph Bredenhann > > > > On Sat, 2011-05-07 at 14:26 -0400, Jeff Squyres wrote: > >> What is the compile line that you are using to compile your application? > >> > >> If you use "mpif90 ...", then the right compiler directive should be > >> automatically added such that the mpi module will be found (assuming that > >> your OMPI was installed with F90 support, that is). > >> > >> > >> On May 7, 2011, at 2:09 PM, Steph Bredenhann wrote: > >> > >> > I have compiled all my fortran source files successfully with openmpi > >> > 1.4.3 wrapper for ifort on Ubuntu 10.10, except the main progran file > >> > that contains the "include mpif.h" statement. It seems that the "include > >> > mpif.h" is deprecated and that one should now use "USE mpi". However, > >> > when compiling with this I get the following message: > >> > > >> > Compile... > >> > 3k-1.for(2): error #7002: Error in opening the compiled module file. > >> > Check INCLUDE paths. [MPI] > >> > USE mpi > >> > --^ > >> > compilation aborted for 3k-1.for (code 1) > >> > done > >> > > >> > "/usr/include/mpi" is included in the variable $INCLUDE > >> > > >> > Could someone please advise on the next step to take? > >> > > >> > Thanks > >> > > >> > > >> > > >> > -- > >> > Steph Bredenhann > >> > > >> > ___ > >> > 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 > >
Re: [OMPI users] USE mpi
Sorry, I missed the 2nd statement: Fortran90 bindings: yes Fortran90 bindings size: small Fortran90 compiler: gfortran Fortran90 compiler abs: /usr/bin/gfortran Fortran90 profiling: yes -- Steph Bredenhann On Sat, 2011-05-07 at 14:46 -0400, Jeff Squyres wrote: > ompi_info | grep 90
Re: [OMPI users] Mixing the FORTRAN and C APIs.
In addition to what Tim Prince said: 1. you can mix C and Fortran MPI function calls in a single program 2. as such, there's no reason for your C++ app to call mpi_init__() (for example) 3. you should be able to call *all* MPI C functions as you normally would 4. the only things that you should need MPI__f2c / MPI__c2f for are when you exchange MPI handles between your app and PARPACK. For example, if you have to pass an MPI datatype down to PARPACK, you'd actually need to pass MPI_Type_f2c(MPI_INTEGER), or MPI_Type_f2c(MPI_DOUBLE_PRECISION). 5. yes, it might be a pain to figure out how to link your C++ app with a fortran library, but I think you need to figure that out. You *may* actually end up linking your final executable with the Fortran compiler/linker, not the C++ compiler/linker. But you may need to specify some extra support libraries regardless of which linker you end up using -- you might need to google around and see if other people have tried linking C++ and Fortran together with your compiler suite. Make sense? On May 6, 2011, at 1:50 PM, Tim Prince wrote: > On 5/6/2011 10:22 AM, Tim Hutt wrote: >> On 6 May 2011 16:45, Tim Hutt wrote: >>> On 6 May 2011 16:27, Tim Prince wrote: If you want to use the MPI Fortran library, don't convert your Fortran to C. It's difficult to understand why you would consider f2c a "simplest way," but at least it should allow you to use ordinary C MPI function calls. >>> >>> Sorry, maybe I wasn't clear. Just to clarify, all of *my* code is >>> written in C++ (because I don't actually know Fortran), but I want to >>> use some function from PARPACK which is written in Fortran. >> >> Hmm I converted my C++ code to use the C OpenMPI interface instead, >> and now I get link errors (undefined references). I remembered I've >> been linking with -lmpi -lmpi_f77, so maybe I need to also link with >> -lmpi_cxx or -lmpi++ ... what exactly do each of these libraries >> contain? >> >> Also I have run into the problem that the communicators are of type >> "MPI_Comm" in C, and "integer" in Fortran... I am using MPI_COMM_WORLD >> in each case so I assume that will end up referring to the same >> thing... but maybe you really can't mix Fortran and C. Expert opinion >> would be very very welcome! >> > If you use your OpenMPI mpicc wrapper to compile and link, the MPI libraries > should be taken care of. > Style usage in an f2c translation is debatable, but you have an #include > "f2c.h" or "g2c.h" which translates the Fortran data types to legacy C > equivalent. By legacy I mean that in the f2c era, the inclusion of C data > types in Fortran via USE iso_c_binding had not been envisioned. > One would think that you would use the MPI header data types on both the > Fortran and the C side, even though you are using legacy interfaces. > Slip-ups in MPI data types often lead to run-time errors. If you have an > error-checking MPI library such as the Intel MPI one, you get a little better > explanation at the failure point. > -- > Tim Prince > ___ > 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] USE mpi
We iterated off-list -- the problem was that "sudo make install" didn't find the icc compiler, and therefore didn't complete properly. It seems that the ompi_info and mpif90 cited in this thread were from some other (broken?) OMPI installation. On May 7, 2011, at 3:01 PM, Steph Bredenhann wrote: > Sorry, I missed the 2nd statement: > > Fortran90 bindings: yes > Fortran90 bindings size: small > Fortran90 compiler: gfortran > Fortran90 compiler abs: /usr/bin/gfortran > Fortran90 profiling: yes > > > -- > Steph Bredenhann > > On Sat, 2011-05-07 at 14:46 -0400, Jeff Squyres wrote: >> ompi_info | grep 90 > ___ > 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] Mixing the FORTRAN and C APIs.
On May 7, 2011, at 5:01 PM, Jeff Squyres wrote: > example, if you have to pass an MPI datatype down to PARPACK, you'd actually > need to pass MPI_Type_f2c(MPI_INTEGER), or MPI_Type_f2c(MPI_DOUBLE_PRECISION). Blarg -- I got these backwards. I should have said: > MPI_Type_c2f(MPI_INTEGER), or MPI_Type_c2f(MPI_DOUBLE_PRECISION). Because the MPI_INTEGER and MPI_DOUBLE_PRECISION handles you're using are C handles, and you need to translate them to the equivalent Fortran handles (i.e., the integer handle values you see in mpif.h.). Try it -- cout the return value from MPI_Type_c2f(MPI_INTEGER) and it should match the value you see in mpif.h. -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] USE mpi
> didn't find the icc compiler Jeff, on 1.4.3 I saw the same issue, even more generally: "make install" cannot find the compiler, if it is an alien compiler (i.e. not the default gcc) - same situation for intel or llvm, for example. The workaround is to specify full paths to compilers with CC=... FC=... in ./configure params. Could it be "make install" breaks some env paths? - D. 2011/5/8 Jeff Squyres : > We iterated off-list -- the problem was that "sudo make install" didn't find > the icc compiler, and therefore didn't complete properly. > > It seems that the ompi_info and mpif90 cited in this thread were from some > other (broken?) OMPI installation. > > > > On May 7, 2011, at 3:01 PM, Steph Bredenhann wrote: > >> Sorry, I missed the 2nd statement: >> >> Fortran90 bindings: yes >> Fortran90 bindings size: small >> Fortran90 compiler: gfortran >> Fortran90 compiler abs: /usr/bin/gfortran >> Fortran90 profiling: yes >> >> >> -- >> Steph Bredenhann >> >> On Sat, 2011-05-07 at 14:46 -0400, Jeff Squyres wrote: >>> ompi_info | grep 90 >> ___ >> 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 >
Re: [OMPI users] USE mpi
On 5/7/2011 2:35 PM, Dmitry N. Mikushin wrote: didn't find the icc compiler Jeff, on 1.4.3 I saw the same issue, even more generally: "make install" cannot find the compiler, if it is an alien compiler (i.e. not the default gcc) - same situation for intel or llvm, for example. The workaround is to specify full paths to compilers with CC=... FC=... in ./configure params. Could it be "make install" breaks some env paths? Most likely reason for not finding an installed icc is that the icc environment (source the compilervars script if you have a current version) wasn't set prior to running configure. Setting up the compiler in question in accordance with its own instructions is a more likely solution than the absolute path choice. OpenMPI configure, for good reason, doesn't search your system to see where a compiler might be installed. What if you had 2 versions of the same named compiler? -- Tim Prince
Re: [OMPI users] USE mpi
Tim, I certainly do not expect anything special, just normally "make install" should not have issues, if "make" passes fine, right? What we have with OpenMPI is this strange difference: if ./configure CC=icc, "make" works, and "make install" - does not; if ./configure CC=/full/path/to/icc, then both "make" and "make install" work. Nothing needs to be searched, icc is already in PATH, since compilevars are sourced in profile.d. Or am I missing something? Thanks, - D. 2011/5/8 Tim Prince : > On 5/7/2011 2:35 PM, Dmitry N. Mikushin wrote: >>> >>> didn't find the icc compiler >> >> Jeff, on 1.4.3 I saw the same issue, even more generally: "make >> install" cannot find the compiler, if it is an alien compiler (i.e. >> not the default gcc) - same situation for intel or llvm, for example. >> The workaround is to specify full paths to compilers with CC=... >> FC=... in ./configure params. Could it be "make install" breaks some >> env paths? >> > > Most likely reason for not finding an installed icc is that the icc > environment (source the compilervars script if you have a current version) > wasn't set prior to running configure. Setting up the compiler in question > in accordance with its own instructions is a more likely solution than the > absolute path choice. > OpenMPI configure, for good reason, doesn't search your system to see where > a compiler might be installed. What if you had 2 versions of the same named > compiler? > -- > Tim Prince > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
