October 2015 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Balaji, Pavan 15 Oct '15

15 Oct '15

Yanfei, Ken, Notice that the user is having trouble because the SLURM path is not passed to the mpich test suite (not mpich itself). My guess is that we did something weird in passing the paths downstream since setting xFLAGS didn't help the user either. -- Pavan On 10/15/15, 10:37 AM, "Guo, Yanfei" <yguo(a)anl.gov> wrote: >Then, can you check if “/usr/scheduler/slurm/lib” is in ld’s search path. You can get that by running ldconfig -v 2>/dev/null | grep -v ^$'\t’ > >If not, you will need to set >LIBRARY_PATH=“/usr/scheduler/slurm/lib” >LD_LIBRARY_PATH=“/usr/scheduler/slurm/lib” > > >Yanfei Guo >Postdoctoral Appointee >MCS Division, ANL > > > > > > > >On 10/15/15, 10:34 AM, "Kenneth Raffenetti" <raffenet(a)mcs.anl.gov> wrote: > >>I think this is the right solution, but should actually be >>"—with-slurm=/usr/scheduler/slurm". See the help text from configure: >> >> -with-slurm=PATH specify path where slurm include directory and >>lib directory can be found >> >>Ken >> >>On 10/15/2015 10:25 AM, Guo, Yanfei wrote: >>> Can you try using “—with-slurm=/usr/scheduler/slurm/lib” when you run ./configure? >>> >>> Yanfei Guo >>> Postdoctoral Appointee >>> MCS Division, ANL >>> >>> >>> >>> >>> >>> >>> >>> On 10/14/15, 3:21 PM, "Davide Vanzo" <vanzod(a)accre.vanderbilt.edu> wrote: >>> >>>> Pavan, >>>> maybe you missed in the crowd of my previous email. Anyway, yes, the library is there: >>>> >>>> >>>> $ ls /usr/scheduler/slurm/lib >>>> libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 >>>> libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 >>>> libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm >>>> libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 >>>> libpmi2.so.0.0.0 libslurm.a libslurm.la >>>> libpmi.a libslurmdb.a libslurm.so >>>> >>>> >>>> Davide >>>> >>>> >>>> >>>> >>>> On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: >>>> >>>> >>>> >>>> Can you make sure you have SLURM's libpmi in the location you specified below (/usr/scheduler/slurm/lib)? >>>> >>>> >>>> -- Pavan >>>> >>>> >>>> >>>> >>>> >>>> From: Davide Vanzo >>>> Reply-To: "discuss(a)mpich.org" >>>> Date: Wednesday, October 14, 2015 at 2:29 PM >>>> To: "discuss(a)mpich.org" >>>> Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 >>>> >>>> >>>> >>>> Hello all, >>>> I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. >>>> I followed the guide and I added the slurm flags to configure as follows: >>>> >>>> >>>> >>>> >>>> ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm >>>> >>>> >>>> >>>> >>>> The only compiler options I'm using are: >>>> >>>> >>>> MPICHLIB_xFLAGS="-O3 -march=corei7" >>>> >>>> >>>> >>>> >>>> MPICH builds correctly, but when I run make testing, I get the following error: >>>> >>>> >>>> >>>> >>>> ( cd test && make testing ) >>>> make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' >>>> (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) >>>> make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' >>>> ./runtests -srcdir=. -tests=testlist \ >>>> -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec -xmlfile=summary.xml \ >>>> -tapfile=summary.tap -junitfile=summary.junit.xml >>>> Looking in ./testlist >>>> Processing directory attr >>>> Looking in ./attr/testlist >>>> Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >>>> CC attrt.o >>>> CCLD attrt >>>> /usr/bin/ld: cannot find -lpmi >>>> collect2: ld returned 1 exit status >>>> make[3]: *** [attrt] Error 1 >>>> make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >>>> >>>> >>>> >>>> >>>> although /usr/scheduler/slurm/lib/libpmi.la exists. >>>> So I tried to explicitly use the lib and include path in the configure options: no luck. >>>> I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. >>>> Any suggestion? >>>> Please let me know if I missed some information and thank you in advance for your help. >>>> >>>> >>>> Best regards, >>>> Davide >>>> >>>> >>>> -- >>>> Davide Vanzo, PhD >>>> Application Developer >>>> Advanced Computing Center for Research and Education (ACCRE) >>>> Vanderbilt University - Hill Center 201 >>>> www.accre.vanderbilt.edu <http://www.accre.vanderbilt.edu/> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>_______________________________________________ >>discuss mailing list discuss(a)mpich.org >>To manage subscription options or unsubscribe: >>https://lists.mpich.org/mailman/listinfo/discuss >_______________________________________________ >discuss mailing list discuss(a)mpich.org >To manage subscription options or unsubscribe: >https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Guo, Yanfei 15 Oct '15

15 Oct '15

Then, can you check if “/usr/scheduler/slurm/lib” is in ld’s search path. You can get that by running ldconfig -v 2>/dev/null | grep -v ^$'\t’ If not, you will need to set LIBRARY_PATH=“/usr/scheduler/slurm/lib” LD_LIBRARY_PATH=“/usr/scheduler/slurm/lib” Yanfei Guo Postdoctoral Appointee MCS Division, ANL On 10/15/15, 10:34 AM, "Kenneth Raffenetti" <raffenet(a)mcs.anl.gov> wrote: >I think this is the right solution, but should actually be >"—with-slurm=/usr/scheduler/slurm". See the help text from configure: > > -with-slurm=PATH specify path where slurm include directory and >lib directory can be found > >Ken > >On 10/15/2015 10:25 AM, Guo, Yanfei wrote: >> Can you try using “—with-slurm=/usr/scheduler/slurm/lib” when you run ./configure? >> >> Yanfei Guo >> Postdoctoral Appointee >> MCS Division, ANL >> >> >> >> >> >> >> >> On 10/14/15, 3:21 PM, "Davide Vanzo" <vanzod(a)accre.vanderbilt.edu> wrote: >> >>> Pavan, >>> maybe you missed in the crowd of my previous email. Anyway, yes, the library is there: >>> >>> >>> $ ls /usr/scheduler/slurm/lib >>> libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 >>> libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 >>> libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm >>> libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 >>> libpmi2.so.0.0.0 libslurm.a libslurm.la >>> libpmi.a libslurmdb.a libslurm.so >>> >>> >>> Davide >>> >>> >>> >>> >>> On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: >>> >>> >>> >>> Can you make sure you have SLURM's libpmi in the location you specified below (/usr/scheduler/slurm/lib)? >>> >>> >>> -- Pavan >>> >>> >>> >>> >>> >>> From: Davide Vanzo >>> Reply-To: "discuss(a)mpich.org" >>> Date: Wednesday, October 14, 2015 at 2:29 PM >>> To: "discuss(a)mpich.org" >>> Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 >>> >>> >>> >>> Hello all, >>> I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. >>> I followed the guide and I added the slurm flags to configure as follows: >>> >>> >>> >>> >>> ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm >>> >>> >>> >>> >>> The only compiler options I'm using are: >>> >>> >>> MPICHLIB_xFLAGS="-O3 -march=corei7" >>> >>> >>> >>> >>> MPICH builds correctly, but when I run make testing, I get the following error: >>> >>> >>> >>> >>> ( cd test && make testing ) >>> make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' >>> (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) >>> make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' >>> ./runtests -srcdir=. -tests=testlist \ >>> -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec -xmlfile=summary.xml \ >>> -tapfile=summary.tap -junitfile=summary.junit.xml >>> Looking in ./testlist >>> Processing directory attr >>> Looking in ./attr/testlist >>> Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >>> CC attrt.o >>> CCLD attrt >>> /usr/bin/ld: cannot find -lpmi >>> collect2: ld returned 1 exit status >>> make[3]: *** [attrt] Error 1 >>> make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >>> >>> >>> >>> >>> although /usr/scheduler/slurm/lib/libpmi.la exists. >>> So I tried to explicitly use the lib and include path in the configure options: no luck. >>> I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. >>> Any suggestion? >>> Please let me know if I missed some information and thank you in advance for your help. >>> >>> >>> Best regards, >>> Davide >>> >>> >>> -- >>> Davide Vanzo, PhD >>> Application Developer >>> Advanced Computing Center for Research and Education (ACCRE) >>> Vanderbilt University - Hill Center 201 >>> www.accre.vanderbilt.edu <http://www.accre.vanderbilt.edu/> >>> >>> >>> >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> >_______________________________________________ >discuss mailing list discuss(a)mpich.org >To manage subscription options or unsubscribe: >https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH symmetric mode execution on Xeon Phi
by Durnov, Dmitry 15 Oct '15

15 Oct '15

Hello Mahdieh, There was a related discussion recently: link<http://lists.mpich.org/pipermail/discuss/2015-September/004175.html> You may try similar approach if I’ve got your question in the correct way. BR, Dmitry From: mahdiyeh ghazi [mailto:[email protected]] Sent: Thursday, October 15, 2015 5:44 PM To: discuss(a)mpich.org Subject: [mpich-discuss] MPICH symmetric mode execution on Xeon Phi Hi, I'm trying to use MPICH to run a code in symmetric mode on Xeon Phi. First, I installed MPICH-3.1.4 with the following configuration for Xeon Phi: ./configure --prefix=/opt/new-mpich/mpich-3.1.4/1 --with-device=ch3:nemesis --host=x86_64 --build=x86_64-k1om-linux CC=icc CXX=icpc --disable-f77 --disable-fc CFLAGS=-mmic CXXFLAGS=-mmic --disable-mcast --disable-fortran LDFLAGS='-L/home/ghazim/build/aster/intel/composer_xe_2015.3.187/compiler/lib/mic/ -Wl,-rpath,/home/ghazim/build/aster/intel/composer_xe_2015.3.187/compiler/lib/mic/' With this configuration, I could successfully run a code in native mode on Xeon Phi. In order to run the code in symmetric mode, I installed MPICH once again, this time for the host with following configuration: ./configure --prefix=/opt/new-mpich-host/mpich-3.1.4/1 Then I compiled the code two times, once with -mmic option to make executable for Xeon Phi (from /opt/new-mpich/mpich-3.1.4/1) and once again without -mmic option to make executable for the host (from /opt/new-mpich-host/mpich-3.1.4/1). Now, my question is how I can run the program with these two executable from Xeon Phi and the host. I know that MPICH supports running parallel programs with different executables with some devices like ch_p4, ch_mpl and globus2 using MPMD but I don't know how I can use this feature to run the code in symmetric mode on Xeon Phi and whether it is possible or not. Thanks, Mahdieh -------------------------------------------------------------------- Joint Stock Company Intel A/O Registered legal address: Krylatsky Hills Business Park, 17 Krylatskaya Str., Bldg 4, Moscow 121614, Russian Federation This e-mail and any attachments may contain confidential material for the sole use of the intended recipient(s). Any review or distribution by others is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Kenneth Raffenetti 15 Oct '15

15 Oct '15

I think this is the right solution, but should actually be "—with-slurm=/usr/scheduler/slurm". See the help text from configure: -with-slurm=PATH specify path where slurm include directory and lib directory can be found Ken On 10/15/2015 10:25 AM, Guo, Yanfei wrote: > Can you try using “—with-slurm=/usr/scheduler/slurm/lib” when you run ./configure? > > Yanfei Guo > Postdoctoral Appointee > MCS Division, ANL > > > > > > > > On 10/14/15, 3:21 PM, "Davide Vanzo" <vanzod(a)accre.vanderbilt.edu> wrote: > >> Pavan, >> maybe you missed in the crowd of my previous email. Anyway, yes, the library is there: >> >> >> $ ls /usr/scheduler/slurm/lib >> libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 >> libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 >> libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm >> libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 >> libpmi2.so.0.0.0 libslurm.a libslurm.la >> libpmi.a libslurmdb.a libslurm.so >> >> >> Davide >> >> >> >> >> On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: >> >> >> >> Can you make sure you have SLURM's libpmi in the location you specified below (/usr/scheduler/slurm/lib)? >> >> >> -- Pavan >> >> >> >> >> >> From: Davide Vanzo >> Reply-To: "discuss(a)mpich.org" >> Date: Wednesday, October 14, 2015 at 2:29 PM >> To: "discuss(a)mpich.org" >> Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 >> >> >> >> Hello all, >> I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. >> I followed the guide and I added the slurm flags to configure as follows: >> >> >> >> >> ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm >> >> >> >> >> The only compiler options I'm using are: >> >> >> MPICHLIB_xFLAGS="-O3 -march=corei7" >> >> >> >> >> MPICH builds correctly, but when I run make testing, I get the following error: >> >> >> >> >> ( cd test && make testing ) >> make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' >> (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) >> make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' >> ./runtests -srcdir=. -tests=testlist \ >> -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec -xmlfile=summary.xml \ >> -tapfile=summary.tap -junitfile=summary.junit.xml >> Looking in ./testlist >> Processing directory attr >> Looking in ./attr/testlist >> Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >> CC attrt.o >> CCLD attrt >> /usr/bin/ld: cannot find -lpmi >> collect2: ld returned 1 exit status >> make[3]: *** [attrt] Error 1 >> make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >> >> >> >> >> although /usr/scheduler/slurm/lib/libpmi.la exists. >> So I tried to explicitly use the lib and include path in the configure options: no luck. >> I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. >> Any suggestion? >> Please let me know if I missed some information and thank you in advance for your help. >> >> >> Best regards, >> Davide >> >> >> -- >> Davide Vanzo, PhD >> Application Developer >> Advanced Computing Center for Research and Education (ACCRE) >> Vanderbilt University - Hill Center 201 >> www.accre.vanderbilt.edu <http://www.accre.vanderbilt.edu/> >> >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Guo, Yanfei 15 Oct '15

15 Oct '15

Can you try using “—with-slurm=/usr/scheduler/slurm/lib” when you run ./configure? Yanfei Guo Postdoctoral Appointee MCS Division, ANL On 10/14/15, 3:21 PM, "Davide Vanzo" <vanzod(a)accre.vanderbilt.edu> wrote: >Pavan, >maybe you missed in the crowd of my previous email. Anyway, yes, the library is there: > > >$ ls /usr/scheduler/slurm/lib >libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 >libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 >libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm >libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 >libpmi2.so.0.0.0 libslurm.a libslurm.la >libpmi.a libslurmdb.a libslurm.so > > >Davide > > > > >On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: > > > >Can you make sure you have SLURM's libpmi in the location you specified below (/usr/scheduler/slurm/lib)? > > > -- Pavan > > > > > >From: Davide Vanzo >Reply-To: "discuss(a)mpich.org" >Date: Wednesday, October 14, 2015 at 2:29 PM >To: "discuss(a)mpich.org" >Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 > > > >Hello all, >I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. >I followed the guide and I added the slurm flags to configure as follows: > > > > >./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm > > > > >The only compiler options I'm using are: > > >MPICHLIB_xFLAGS="-O3 -march=corei7" > > > > >MPICH builds correctly, but when I run make testing, I get the following error: > > > > >( cd test && make testing ) >make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' >(NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) >make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' >./runtests -srcdir=. -tests=testlist \ >-mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec -xmlfile=summary.xml \ >-tapfile=summary.tap -junitfile=summary.junit.xml >Looking in ./testlist >Processing directory attr >Looking in ./attr/testlist >Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' > CC attrt.o > CCLD attrt >/usr/bin/ld: cannot find -lpmi >collect2: ld returned 1 exit status >make[3]: *** [attrt] Error 1 >make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' > > > > >although /usr/scheduler/slurm/lib/libpmi.la exists. >So I tried to explicitly use the lib and include path in the configure options: no luck. >I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. >Any suggestion? >Please let me know if I missed some information and thank you in advance for your help. > > >Best regards, >Davide > > >-- >Davide Vanzo, PhD >Application Developer >Advanced Computing Center for Research and Education (ACCRE) >Vanderbilt University - Hill Center 201 >www.accre.vanderbilt.edu <http://www.accre.vanderbilt.edu/> > > > > >_______________________________________________ >discuss mailing list discuss(a)mpich.org >To manage subscription options or unsubscribe: >https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Kenneth Raffenetti 15 Oct '15

15 Oct '15

What does the output of your "mpicc -show" look like? On 10/14/2015 03:21 PM, Davide Vanzo wrote: > Pavan, > maybe you missed in the crowd of my previous email. Anyway, yes, the > library is there: > > $ ls /usr/scheduler/slurm/lib > libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 > libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 > libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm > libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 > libpmi2.so.0.0.0 libslurm.a libslurm.la > libpmi.a libslurmdb.a libslurm.so > > Davide > > > On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: >> >> Can you make sure you have SLURM's libpmi in the location you >> specified below (/usr/scheduler/slurm/lib)? >> >> -- Pavan >> >> From: Davide Vanzo >> Reply-To: "discuss(a)mpich.org <mailto:[email protected]>" >> Date: Wednesday, October 14, 2015 at 2:29 PM >> To: "discuss(a)mpich.org <mailto:[email protected]>" >> Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 >> >> Hello all, >> I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system >> with Slurm 14.11.9. I want to test the performance fall when using >> srun vs. mpiexec.hydra. >> I followed the guide and I added the slurm flags to configure as follows: >> >> >> ./configure --with-device=ch3:nemesis --prefix=$PREFIX >> --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm >> --with-pm=no --with-slurm=/usr/scheduler/slurm >> >> >> The only compiler options I'm using are: >> >> MPICHLIB_xFLAGS="-O3 -march=corei7" >> >> >> MPICH builds correctly, but when I run make testing, I get the >> following error: >> >> >> ( cd test && make testing ) >> make[1]: Entering directory >> `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' >> (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) >> make[2]: Entering directory >> `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' >> ./runtests -srcdir=. -tests=testlist \ >> -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec >> -xmlfile=summary.xml \ >> -tapfile=summary.tap -junitfile=summary.junit.xml >> Looking in ./testlist >> Processing directory attr >> Looking in ./attr/testlist >> Failed to build attrt; make[3]: Entering directory >> `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >> CC attrt.o >> CCLD attrt >> /usr/bin/ld: cannot find -lpmi >> collect2: ld returned 1 exit status >> make[3]: *** [attrt] Error 1 >> make[3]: Leaving directory >> `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' >> >> >> although /usr/scheduler/slurm/lib/libpmi.la exists. >> So I tried to explicitly use the lib and include path in the configure >> options: no luck. >> I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. >> Any suggestion? >> Please let me know if I missed some information and thank you in >> advance for your help. >> >> Best regards, >> Davide >> >> -- >> Davide Vanzo, PhD >> Application Developer >> Advanced Computing Center for Research and Education (ACCRE) >> Vanderbilt University - Hill Center 201 >> www.accre.vanderbilt.edu <http://www.accre.vanderbilt.edu/> >> _______________________________________________ >> discuss mailing listdiscuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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MPICH symmetric mode execution on Xeon Phi
by mahdiyeh ghazi 15 Oct '15

15 Oct '15

Hi, I'm trying to use MPICH to run a code in symmetric mode on Xeon Phi. First, I installed MPICH-3.1.4 with the following configuration for Xeon Phi: ./configure --prefix=/opt/new-mpich/mpich-3.1.4/1 --with-device=ch3:nemesis --host=x86_64 --build=x86_64-k1om-linux CC=icc CXX=icpc --disable-f77 --disable-fc CFLAGS=-mmic CXXFLAGS=-mmic --disable-mcast --disable-fortran LDFLAGS='-L/home/ghazim/build/aster/intel/composer_xe_2015.3.187/compiler/lib/mic/ -Wl,-rpath,/home/ghazim/build/aster/intel/composer_xe_2015.3.187/compiler/lib/mic/' With this configuration, I could successfully run a code in native mode on Xeon Phi. In order to run the code in symmetric mode, I installed MPICH once again, this time for the host with following configuration: ./configure --prefix=/opt/new-mpich-host/mpich-3.1.4/1 Then I compiled the code two times, once with -mmic option to make executable for Xeon Phi (from /opt/new-mpich/mpich-3.1.4/1) and once again without -mmic option to make executable for the host (from /opt/new-mpich-host/mpich-3.1.4/1). Now, my question is how I can run the program with these two executable from Xeon Phi and the host. I know that MPICH supports running parallel programs with different executables with some devices like ch_p4, ch_mpl and globus2 using MPMD but I don't know how I can use this feature to run the code in symmetric mode on Xeon Phi and whether it is possible or not. Thanks, Mahdieh _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Davide Vanzo 14 Oct '15

14 Oct '15

Pavan, maybe you missed in the crowd of my previous email. Anyway, yes, the library is there: $ ls /usr/scheduler/slurm/lib libpmi2.a libpmi.la libslurmdb.la libslurm.so.28 libpmi2.la libpmi.so libslurmdb.so libslurm.so.28.0.0 libpmi2.so libpmi.so.0 libslurmdb.so.28 slurm libpmi2.so.0 libpmi.so.0.0.0 libslurmdb.so.28.0.0 libpmi2.so.0.0.0 libslurm.a libslurm.la libpmi.a libslurmdb.a libslurm.so Davide On Wed, 2015-10-14 at 20:17 +0000, Balaji, Pavan wrote: > > Can you make sure you have SLURM's libpmi in the location you > specified below (/usr/scheduler/slurm/lib)? > > -- Pavan > > From: Davide Vanzo > Reply-To: "discuss(a)mpich.org" > Date: Wednesday, October 14, 2015 at 2:29 PM > To: "discuss(a)mpich.org" > Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 > > Hello all, > I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a > system with Slurm 14.11.9. I want to test the performance fall when > using srun vs. mpiexec.hydra. > I followed the guide and I added the slurm flags to configure as > follows: > > > ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable > -fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with > -pm=no --with-slurm=/usr/scheduler/slurm > > > The only compiler options I'm using are: > > MPICHLIB_xFLAGS="-O3 -march=corei7" > > > MPICH builds correctly, but when I run make testing, I get the > following error: > > > ( cd test && make testing ) > make[1]: Entering directory > `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' > (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) > make[2]: Entering directory > `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mp > i' > ./runtests -srcdir=. -tests=testlist \ > -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec > -xmlfile=summary.xml \ > -tapfile=summary.tap -junitfile=summary.junit.xml > Looking in ./testlist > Processing directory attr > Looking in ./attr/testlist > Failed to build attrt; make[3]: Entering directory > `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mp > i/attr' > CC attrt.o > CCLD attrt > /usr/bin/ld: cannot find -lpmi > collect2: ld returned 1 exit status > make[3]: *** [attrt] Error 1 > make[3]: Leaving directory > `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mp > i/attr' > > > although /usr/scheduler/slurm/lib/libpmi.la exists. > So I tried to explicitly use the lib and include path in the > configure options: no luck. > I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. > Any suggestion? > Please let me know if I missed some information and thank you in > advance for your help. > > Best regards, > Davide > > -- > Davide Vanzo, PhD > Application Developer > Advanced Computing Center for Research and Education (ACCRE) > Vanderbilt University - Hill Center 201 > www.accre.vanderbilt.edu > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9
by Balaji, Pavan 14 Oct '15

14 Oct '15

Can you make sure you have SLURM's libpmi in the location you specified below (/usr/scheduler/slurm/lib)? -- Pavan From: Davide Vanzo Reply-To: "discuss(a)mpich.org<mailto:[email protected]>" Date: Wednesday, October 14, 2015 at 2:29 PM To: "discuss(a)mpich.org<mailto:[email protected]>" Subject: [mpich-discuss] MPICH 3.1.4 with Slurm 14.11.9 Hello all, I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. I followed the guide and I added the slurm flags to configure as follows: ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable-fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm The only compiler options I'm using are: MPICHLIB_xFLAGS="-O3 -march=corei7" MPICH builds correctly, but when I run make testing, I get the following error: ( cd test && make testing ) make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' ./runtests -srcdir=. -tests=testlist \ -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bin/mpiexec -xmlfile=summary.xml \ -tapfile=summary.tap -junitfile=summary.junit.xml Looking in ./testlist Processing directory attr Looking in ./attr/testlist Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' CC attrt.o CCLD attrt /usr/bin/ld: cannot find -lpmi collect2: ld returned 1 exit status make[3]: *** [attrt] Error 1 make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/attr' although /usr/scheduler/slurm/lib/libpmi.la exists. So I tried to explicitly use the lib and include path in the configure options: no luck. I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. Any suggestion? Please let me know if I missed some information and thank you in advance for your help. Best regards, Davide -- Davide Vanzo, PhD Application Developer Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu<http://www.accre.vanderbilt.edu/> _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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MPICH 3.1.4 with Slurm 14.11.9
by Davide Vanzo 14 Oct '15

14 Oct '15

Hello all, I'm trying to compile MPICH 3.1.4 with GNU compilers 4.9.0 on a system with Slurm 14.11.9. I want to test the performance fall when using srun vs. mpiexec.hydra. I followed the guide and I added the slurm flags to configure as follows: ./configure --with-device=ch3:nemesis --prefix=$PREFIX --enable -fortran=yes --enable-cxx --enable-shared --with-pmi=slurm --with-pm=no --with-slurm=/usr/scheduler/slurm The only compiler options I'm using are: MPICHLIB_xFLAGS="-O3 -march=corei7" MPICH builds correctly, but when I run make testing, I get the following error: ( cd test && make testing ) make[1]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test' (NOXMLCLOSE=YES && export NOXMLCLOSE && cd mpi && make testing) make[2]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi' ./runtests -srcdir=. -tests=testlist \ -mpiexec=/usr/local/mpich/3.1.4/nehalem/gcc49/ether/bi n/mpiexec -xmlfile=summary.xml \ -tapfile=summary.tap -junitfile=summary.junit.xml Looking in ./testlist Processing directory attr Looking in ./attr/testlist Failed to build attrt; make[3]: Entering directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/ attr' CC attrt.o CCLD attrt /usr/bin/ld: cannot find -lpmi collect2: ld returned 1 exit status make[3]: *** [attrt] Error 1 make[3]: Leaving directory `/gpfs22/local/centos6/mpich/3.1.4/nehalem/gcc49/ether/source/test/mpi/ attr' although /usr/scheduler/slurm/lib/libpmi.la exists. So I tried to explicitly use the lib and include path in the configure options: no luck. I also set "-L/usr/scheduler/slurm/lib" in the xFLAGS, but no effect. Any suggestion? Please let me know if I missed some information and thank you in advance for your help. Best regards, Davide -- Davide Vanzo, PhD Application Developer Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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