Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Michael, i will followup on that in the devel mailing list. imho, there are three ways to see this : 1) this is an environment (e.g. user) issue: if you want it to work, then slurm should be rebuilt with pgi compiler. 2) this is a libtool issue : it does not support mixing .la files built with gcc and pgcc (e.g. -pthread option is unknown by pgcc) 3) this is an other libtool issue : -noswitcherror should be passed by libtool to the PGI compiler Open MPI is not to be blamed here. that being said, i am pragmatic so i do not mind hacking (one more time ...) libtool in OpenMPI to fix libtool or even make it PGI/GNU friendly Cheers, Gilles On 7/26/2016 2:52 AM, Michael Di Domenico wrote: On Mon, Jul 25, 2016 at 4:53 AM, Gilles Gouaillardet wrote: as a workaround, you can configure without -noswitcherror. after you ran configure, you have to manually patch the generated 'libtool' file and add the line with pgcc*) and the next line like this : /* if pgcc is used, libtool does *not* pass -pthread to pgcc any more */ # Convert "-framework foo" to "foo.ltframework" # and "-pthread" to "-Wl,-pthread" if NAG compiler if test -n "$inherited_linker_flags"; then case "$CC" in nagfor*) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;; pgcc*) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread//g'`;; *) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;; esac i guess the right way is to patch libtool so it passes -noswitcherror to $CC and/or $LD, but i was not able to achieve that yet. Thanks. I managed to work around the issue, by hand compiling the single module that failed during the build process. but something is definitely amiss in the openmpi compile system when it comes to pgi ___ users mailing list us...@open-mpi.org Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/07/29707.php
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
On Mon, Jul 25, 2016 at 4:53 AM, Gilles Gouaillardet wrote: > > as a workaround, you can configure without -noswitcherror. > > after you ran configure, you have to manually patch the generated 'libtool' > file and add the line with pgcc*) and the next line like this : > > /* if pgcc is used, libtool does *not* pass -pthread to pgcc any more */ > > ># Convert "-framework foo" to "foo.ltframework" > # and "-pthread" to "-Wl,-pthread" if NAG compiler > if test -n "$inherited_linker_flags"; then > case "$CC" in > nagfor*) > tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | > $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED > 's/-pthread/-Wl,-pthread/g'`;; > pgcc*) > tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | > $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread//g'`;; > *) > tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | > $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;; > esac > > > i guess the right way is to patch libtool so it passes -noswitcherror to $CC > and/or $LD, but i was not able to achieve that yet. Thanks. I managed to work around the issue, by hand compiling the single module that failed during the build process. but something is definitely amiss in the openmpi compile system when it comes to pgi
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Michael, as a workaround, you can configure without -noswitcherror. after you ran configure, you have to manually patch the generated 'libtool' file and add the line with pgcc*) and the next line like this : /* if pgcc is used, libtool does *not* pass -pthread to pgcc any more */ # Convert "-framework foo" to "foo.ltframework" # and "-pthread" to "-Wl,-pthread" if NAG compiler if test -n "$inherited_linker_flags"; then case "$CC" in nagfor*) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;; pgcc*) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread//g'`;; *) tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;; esac i guess the right way is to patch libtool so it passes -noswitcherror to $CC and/or $LD, but i was not able to achieve that yet. Cheers, Gilles On 7/23/2016 12:31 AM, Michael Di Domenico wrote: So, the -noswitcherror is partially working. I added the switch into my configure line LDFLAGS param. I can see the parameter being passed to libtool, but for some reason libtool is refusing to passing it along at compile. if i sh -x the libtool command line, i can see it set in a few variables, but at the end when eval's the compile line for pgcc the option is missing. if i cut and past the eval line and hand put it back in, the library compiles with a pgcc warning instead of an error which i believe what i want, but i'm not sure why libtool is dropping the switch On Tue, Jul 19, 2016 at 5:27 AM, Sylvain Jeaugey wrote: As a workaround, you can also try adding -noswitcherror to PGCC flags. On 07/11/2016 03:52 PM, Åke Sandgren wrote: Looks like you are compiling with slurm support. If so, you need to remove the "-pthread" from libslurm.la and libpmi.la On 07/11/2016 02:54 PM, Michael Di Domenico wrote: I'm trying to get openmpi compiled using the PGI compiler. the configure goes through and the code starts to compile, but then gets hung up with entering: openmpi-1.10.2/opal/mca/common/pmi CC common_pmi.lo CCLD libmca_common_pmi.la pgcc-Error-Unknown switch: - pthread ___ users mailing list us...@open-mpi.org Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/07/29635.php --- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. --- ___ users mailing list us...@open-mpi.org Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/07/29692.php ___ users mailing list us...@open-mpi.org Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/07/29702.php
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
So, the -noswitcherror is partially working. I added the switch into my configure line LDFLAGS param. I can see the parameter being passed to libtool, but for some reason libtool is refusing to passing it along at compile. if i sh -x the libtool command line, i can see it set in a few variables, but at the end when eval's the compile line for pgcc the option is missing. if i cut and past the eval line and hand put it back in, the library compiles with a pgcc warning instead of an error which i believe what i want, but i'm not sure why libtool is dropping the switch On Tue, Jul 19, 2016 at 5:27 AM, Sylvain Jeaugey wrote: > As a workaround, you can also try adding -noswitcherror to PGCC flags. > > On 07/11/2016 03:52 PM, Åke Sandgren wrote: >> >> Looks like you are compiling with slurm support. >> >> If so, you need to remove the "-pthread" from libslurm.la and libpmi.la >> >> On 07/11/2016 02:54 PM, Michael Di Domenico wrote: >>> >>> I'm trying to get openmpi compiled using the PGI compiler. >>> >>> the configure goes through and the code starts to compile, but then >>> gets hung up with >>> >>> entering: openmpi-1.10.2/opal/mca/common/pmi >>> CC common_pmi.lo >>> CCLD libmca_common_pmi.la >>> pgcc-Error-Unknown switch: - pthread >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/07/29635.php >>> > > --- > This email message is for the sole use of the intended recipient(s) and may > contain > confidential information. Any unauthorized review, use, disclosure or > distribution > is prohibited. If you are not the intended recipient, please contact the > sender by > reply email and destroy all copies of the original message. > --- > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29692.php
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
As a workaround, you can also try adding -noswitcherror to PGCC flags. On 07/11/2016 03:52 PM, Åke Sandgren wrote: Looks like you are compiling with slurm support. If so, you need to remove the "-pthread" from libslurm.la and libpmi.la On 07/11/2016 02:54 PM, Michael Di Domenico wrote: I'm trying to get openmpi compiled using the PGI compiler. the configure goes through and the code starts to compile, but then gets hung up with entering: openmpi-1.10.2/opal/mca/common/pmi CC common_pmi.lo CCLD libmca_common_pmi.la pgcc-Error-Unknown switch: - pthread ___ users mailing list us...@open-mpi.org Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/07/29635.php --- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. ---
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Hello, On 07/11/2016 02:54 PM, Michael Di Domenico wrote: pgcc-Error-Unknown switch: - pthread you want to use -noswitcherror in CFLAGS to work around the problem or edit the .la files as suggested. Alternatively, you can also use a wrapper that strips the -pthread option. Regards, Thomas -- Thomas Jahns HD(CP)^2 Abteilung Anwendungssoftware Deutsches Klimarechenzentrum GmbH Bundesstraße 45a • D-20146 Hamburg • Germany Phone: +49 40 460094-151 Fax:+49 40 460094-270 Email: Thomas Jahns URL:www.dkrz.de Geschäftsführer: Prof. Dr. Thomas Ludwig Sitz der Gesellschaft: Hamburg Amtsgericht Hamburg HRB 39784 smime.p7s Description: S/MIME Cryptographic Signature
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
You can also simply copy slurm (omitting the .la) into an other directory, remove the .la, and pass this directory to Open MPI an other option is to compile slurm with PGI compilers, so your *.la should work fine. You might be luckier by rebuilding slurm with gnu compilers and CFLAGS=-D_REENTRANT LDFLAGS=-lpthread Hopefully slurm will not add the -pthread option Cheers, Gilles On Thursday, July 14, 2016, Michael Di Domenico wrote: > On Mon, Jul 11, 2016 at 9:52 AM, Åke Sandgren > wrote: > > Looks like you are compiling with slurm support. > > > > If so, you need to remove the "-pthread" from libslurm.la and libpmi.la > > i don't see a configure option in slurm to disable pthreads, so i'm > not sure this is possible. > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29664.php
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
No, you have to manually edit those two .la files by hand after installation. It's basically a libtool problem. It generates the .la file with an option that PGI dsoesn't understand. On 07/14/2016 04:06 PM, Michael Di Domenico wrote: > On Mon, Jul 11, 2016 at 9:52 AM, Åke Sandgren > wrote: >> Looks like you are compiling with slurm support. >> >> If so, you need to remove the "-pthread" from libslurm.la and libpmi.la > > i don't see a configure option in slurm to disable pthreads, so i'm > not sure this is possible. -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
On Mon, Jul 11, 2016 at 9:52 AM, Åke Sandgren wrote: > Looks like you are compiling with slurm support. > > If so, you need to remove the "-pthread" from libslurm.la and libpmi.la i don't see a configure option in slurm to disable pthreads, so i'm not sure this is possible.
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
On Thu, Jul 14, 2016 at 9:47 AM, Michael Di Domenico wrote: > Have 1.10.3 unpacked, ran through the configure using the same command > line options as 1.10.2 > > but it fails even earlier in the make process at > > Entering openmpi-1.10.3/opal/asm > CPPAS atomic-asm.lo > This licensed Software was made available from Nvidia Corportation > under a time-limited beta license the beta license expires on jun 1 2015 > any attempt to use this product after jun 1 2015 is a violation of the terms > of the PGI end user license agreement. sorry, i take this back, i accidentally used PGI 15.3 compiler instead of 15.9 using 15.9 i get the same -pthread error from the slurm_pmi library.
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Have 1.10.3 unpacked, ran through the configure using the same command line options as 1.10.2 but it fails even earlier in the make process at Entering openmpi-1.10.3/opal/asm CPPAS atomic-asm.lo This licensed Software was made available from Nvidia Corportation under a time-limited beta license the beta license expires on jun 1 2015 any attempt to use this product after jun 1 2015 is a violation of the terms of the PGI end user license agreement. On Mon, Jul 11, 2016 at 9:11 AM, Gilles Gouaillardet wrote: > Can you try the latest 1.10.3 instead ? > > btw, do you have a license for the pgCC C++ compiler ? > fwiw, FreePGI on OSX has no C++ license and PGI C and gnu g++ does not work > together out of the box, hopefully I will have a fix ready sometimes this > week > > Cheers, > > Gilles > > > On Monday, July 11, 2016, Michael Di Domenico > wrote: >> >> I'm trying to get openmpi compiled using the PGI compiler. >> >> the configure goes through and the code starts to compile, but then >> gets hung up with >> >> entering: openmpi-1.10.2/opal/mca/common/pmi >> CC common_pmi.lo >> CCLD libmca_common_pmi.la >> pgcc-Error-Unknown switch: - pthread >> ___ >> users mailing list >> us...@open-mpi.org >> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/07/29635.php > > > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29636.php
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Looks like you are compiling with slurm support. If so, you need to remove the "-pthread" from libslurm.la and libpmi.la On 07/11/2016 02:54 PM, Michael Di Domenico wrote: > I'm trying to get openmpi compiled using the PGI compiler. > > the configure goes through and the code starts to compile, but then > gets hung up with > > entering: openmpi-1.10.2/opal/mca/common/pmi > CC common_pmi.lo > CCLD libmca_common_pmi.la > pgcc-Error-Unknown switch: - pthread > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29635.php > -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
On Mon, Jul 11, 2016 at 9:11 AM, Gilles Gouaillardet wrote: > Can you try the latest 1.10.3 instead ? i can but it'll take a few days to pull the software inside. > btw, do you have a license for the pgCC C++ compiler ? > fwiw, FreePGI on OSX has no C++ license and PGI C and gnu g++ does not work > together out of the box, hopefully I will have a fix ready sometimes this > week we should, but i'm not positive. we're running PGI on linux x64, we typically buy the full suite, but i'll double check.
Re: [OMPI users] openmpi 1.10.2 and PGI 15.9
Can you try the latest 1.10.3 instead ? btw, do you have a license for the pgCC C++ compiler ? fwiw, FreePGI on OSX has no C++ license and PGI C and gnu g++ does not work together out of the box, hopefully I will have a fix ready sometimes this week Cheers, Gilles On Monday, July 11, 2016, Michael Di Domenico wrote: > I'm trying to get openmpi compiled using the PGI compiler. > > the configure goes through and the code starts to compile, but then > gets hung up with > > entering: openmpi-1.10.2/opal/mca/common/pmi > CC common_pmi.lo > CCLD libmca_common_pmi.la > pgcc-Error-Unknown switch: - pthread > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29635.php >