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Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 09 Jun '13

09 Jun '13

Pavan The words you wanted to see ... biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ salloc -N 1 -n2 salloc: Granted job allocation 25 biddisco@breno2 ~/build/mpich-master-v3.0.4-294-ga5719ca8 $ ./install/bin/mpiexec -n 2 ./hello Hello world from process 0 of 2 Hello world from process 1 of 2 Thank you very much indeed. Not only a very welcome fix, but done at the weekend too! Great work. Thanks again. JB -----Original Message----- From: Pavan Balaji [mailto:[email protected]] Sent: 09 June 2013 17:17 To: Biddiscombe, John A. Cc: discuss(a)mpich.org Subject: Re: [mpich-discuss] Problems running MPICH jobs under SLURM On 06/09/2013 01:03 AM, Biddiscombe, John A. wrote: > For reasons unclear to me, With this tarball, I get no mpiexec compiled. > > I'm doing a diff between the latest tarballs and trying to find the problem ... > > JB > > ll install/bin/ > total 68 > lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx > -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc -rwxr-xr-x 1 > biddisco biddisco 9300 Jun 9 07:55 mpichversion -rwxr-xr-x 1 > biddisco biddisco 9458 Jun 9 07:55 mpicxx -rwxr-xr-x 1 biddisco > biddisco 11551 Jun 9 07:55 mpif77 -rwxr-xr-x 1 biddisco biddisco > 13375 Jun 9 07:55 mpif90 -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 > 07:55 parkill Gah. Sorry about that. Can you try once more? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 09 Jun '13

09 Jun '13

On 06/09/2013 01:03 AM, Biddiscombe, John A. wrote: > For reasons unclear to me, With this tarball, I get no mpiexec compiled. > > I'm doing a diff between the latest tarballs and trying to find the problem ... > > JB > > ll install/bin/ > total 68 > lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx > -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc > -rwxr-xr-x 1 biddisco biddisco 9300 Jun 9 07:55 mpichversion > -rwxr-xr-x 1 biddisco biddisco 9458 Jun 9 07:55 mpicxx > -rwxr-xr-x 1 biddisco biddisco 11551 Jun 9 07:55 mpif77 > -rwxr-xr-x 1 biddisco biddisco 13375 Jun 9 07:55 mpif90 > -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 07:55 parkill Gah. Sorry about that. Can you try once more? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 09 Jun '13

09 Jun '13

For reasons unclear to me, With this tarball, I get no mpiexec compiled. I'm doing a diff between the latest tarballs and trying to find the problem ... JB ll install/bin/ total 68 lrwxrwxrwx 1 biddisco biddisco 6 Jun 9 07:55 mpic++ -> mpicxx -rwxr-xr-x 1 biddisco biddisco 9905 Jun 9 07:55 mpicc -rwxr-xr-x 1 biddisco biddisco 9300 Jun 9 07:55 mpichversion -rwxr-xr-x 1 biddisco biddisco 9458 Jun 9 07:55 mpicxx -rwxr-xr-x 1 biddisco biddisco 11551 Jun 9 07:55 mpif77 -rwxr-xr-x 1 biddisco biddisco 13375 Jun 9 07:55 mpif90 -rwxr-xr-x 1 biddisco biddisco 3430 Jun 9 07:55 parkill -----Original Message----- From: Pavan Balaji [mailto:[email protected]] Sent: 09 June 2013 07:13 To: discuss(a)mpich.org Cc: Biddiscombe, John A. Subject: Re: [mpich-discuss] Problems running MPICH jobs under SLURM John, Can you try the latest nightly snapshot? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan On 06/08/2013 03:23 PM, Pavan Balaji wrote: > > Thanks, John. I'll look into it and get back to you if I need any > more information. > > Btw, you should not need sudo at all. You might have some previously > left over files with root permissions that might have caused the issue. > If you delete the entire directory and start from scratch, this > issue should not be there. > > -- Pavan > > On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: >> Following your instructions (I only have 1 node, so changed N2 n4 to >> N >> 1 n2), same error, listed below... >> >> [NB . Only one interesting thing is that I cannot do a make as user >> biddisco and have to sudo make as it gives me some permission error >> otherwise mkdir -p >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf >> src/env/mpif90.conf src/env/mpicxx.conf >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': >> Permission denied >> make[3]: *** [install-sysconfDATA] Error 1 >> make[3]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make: *** [install] Error 2 >> ] >> >> JB >> >> biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ >> ./install/bin/mpiexec -n 2 ./hello >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000017b2340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000011e7340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] >> >> ./hello[0x40081e] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] >> >> ./hello[0x40081e] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576 >> d] >> ./hello[0x400719] >> ======= Memory map: ======== >> 00400000-00401000 r-xp 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00600000-00601000 r--p 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00601000-00602000 rw-p 00001000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 017b1000-017d2000 rw-p 00000000 00:00 >> 0 [heap] >> 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 >> 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 >> 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 >> 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/li >> bmpich.so.10.0.4 >> >> 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 >> 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 >> 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 >> 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fff671e5000-7fff67206000 rw-p 00000000 00:00 >> 0 [stack] >> 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 >> 0 [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 >> 0 [vsyscall] >> >> ===================================================================== >> ============== >> >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 6 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> ===================================================================== >> ============== >> >> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) >> This typically refers to a problem with your application. >> Please see the FAQ page for debugging suggestions >> > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 09 Jun '13

09 Jun '13

John, Can you try the latest nightly snapshot? http://www.mpich.org/static/tarballs/nightly/master/mpich/ -- Pavan On 06/08/2013 03:23 PM, Pavan Balaji wrote: > > Thanks, John. I'll look into it and get back to you if I need any more > information. > > Btw, you should not need sudo at all. You might have some previously > left over files with root permissions that might have caused the issue. > If you delete the entire directory and start from scratch, this issue > should not be there. > > -- Pavan > > On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: >> Following your instructions (I only have 1 node, so changed N2 n4 to N >> 1 n2), same error, listed below... >> >> [NB . Only one interesting thing is that I cannot do a make as user >> biddisco and have to sudo make as it gives me some permission error >> otherwise >> mkdir -p >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf >> src/env/mpif90.conf src/env/mpicxx.conf >> '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': >> Permission denied >> /usr/bin/install: cannot remove >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': >> Permission denied >> make[3]: *** [install-sysconfDATA] Error 1 >> make[3]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' >> make: *** [install] Error 2 >> ] >> >> JB >> >> biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ >> ./install/bin/mpiexec -n 2 ./hello >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000017b2340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] >> *** glibc detected *** ./hello: double free or corruption (fasttop): >> 0x00000000011e7340 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] >> >> ./hello[0x40081e] >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] >> >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] >> >> ./hello[0x40081e] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] >> ./hello[0x400719] >> ======= Memory map: ======== >> 00400000-00401000 r-xp 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00600000-00601000 r--p 00000000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 00601000-00602000 rw-p 00001000 08:01 >> 10625669 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello >> 017b1000-017d2000 rw-p 00000000 00:00 >> 0 [heap] >> 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 >> 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 >> 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 >> 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 >> 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 >> 9050343 /lib/x86_64-linux-gnu/librt-2.15.so >> 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 >> 8661134 >> /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 >> 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 >> 9050358 /lib/x86_64-linux-gnu/libc-2.15.so >> 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 >> 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 >> 11675463 >> /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 >> >> 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 >> 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 >> 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 >> 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 >> 9050344 /lib/x86_64-linux-gnu/ld-2.15.so >> 7fff671e5000-7fff67206000 rw-p 00000000 00:00 >> 0 [stack] >> 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 >> 0 [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 >> 0 [vsyscall] >> >> =================================================================================== >> >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 6 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> =================================================================================== >> >> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) >> This typically refers to a problem with your application. >> Please see the FAQ page for debugging suggestions >> > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Pavan Balaji 08 Jun '13

08 Jun '13

Thanks, John. I'll look into it and get back to you if I need any more information. Btw, you should not need sudo at all. You might have some previously left over files with root permissions that might have caused the issue. If you delete the entire directory and start from scratch, this issue should not be there. -- Pavan On 06/08/2013 03:02 PM, Biddiscombe, John A. wrote: > Following your instructions (I only have 1 node, so changed N2 n4 to N 1 n2), same error, listed below... > > [NB . Only one interesting thing is that I cannot do a make as user biddisco and have to sudo make as it gives me some permission error otherwise > mkdir -p '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' > /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf src/env/mpif90.conf src/env/mpicxx.conf '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': Permission denied > /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': Permission denied > make[3]: *** [install-sysconfDATA] Error 1 > make[3]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make[2]: *** [install-am] Error 2 > make[2]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' > make: *** [install] Error 2 > ] > > JB > > biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ ./install/bin/mpiexec -n 2 ./hello > *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000017b2340 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] > *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000011e7340 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] > ./hello[0x40081e] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] > /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] > ./hello[0x40081e] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] > ./hello[0x400719] > ======= Memory map: ======== > 00400000-00401000 r-xp 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 00600000-00601000 r--p 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 00601000-00602000 rw-p 00001000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello > 017b1000-017d2000 rw-p 00000000 00:00 0 [heap] > 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 > 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 > 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so > 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 > 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so > 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 > 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so > 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 > 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 > 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 > 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 > 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 > 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so > 7fff671e5000-7fff67206000 rw-p 00000000 00:00 0 [stack] > 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 0 [vdso] > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 6 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Problems running MPICH jobs under SLURM
by Biddiscombe, John A. 08 Jun '13

08 Jun '13

Following your instructions (I only have 1 node, so changed N2 n4 to N 1 n2), same error, listed below... [NB . Only one interesting thing is that I cannot do a make as user biddisco and have to sudo make as it gives me some permission error otherwise mkdir -p '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' /usr/bin/install -c -m 644 src/env/mpicc.conf src/env/mpif77.conf src/env/mpif90.conf src/env/mpicxx.conf '/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc' /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicc.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif77.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpif90.conf': Permission denied /usr/bin/install: cannot remove `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/etc/mpicxx.conf': Permission denied make[3]: *** [install-sysconfDATA] Error 1 make[3]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79' make: *** [install] Error 2 ] JB biddisco@breno2 ~/build/mpich-master-v3.0.4-259-gf322ce79 $ ./install/bin/mpiexec -n 2 ./hello *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000017b2340 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fcaeb4a2b96] *** glibc detected *** ./hello: double free or corruption (fasttop): 0x00000000011e7340 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fd1a77ddb96] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fd1a7bc75a9] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fd1a7bc1da6] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fd1a7c78f1f] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fd1a7c788be] ./hello[0x40081e] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIDI_Populate_vc_node_ids+0x3f9)[0x7fcaeb88c5a9] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPID_Init+0x136)[0x7fcaeb886da6] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPIR_Init_thread+0x22f)[0x7fcaeb93df1f] /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10(MPI_Init+0xae)[0x7fcaeb93d8be] ./hello[0x40081e] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fcaeb44576d] ./hello[0x400719] ======= Memory map: ======== 00400000-00401000 r-xp 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 00600000-00601000 r--p 00000000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 00601000-00602000 rw-p 00001000 08:01 10625669 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/hello 017b1000-017d2000 rw-p 00000000 00:00 0 [heap] 7fcaeabe1000-7fcaeabe4000 rw-p 00000000 00:00 0 7fcaeabe4000-7fcaeabf9000 r-xp 00000000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeabf9000-7fcaeadf8000 ---p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadf8000-7fcaeadf9000 r--p 00014000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadf9000-7fcaeadfa000 rw-p 00015000 08:01 9047556 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fcaeadfa000-7fcaeae12000 r-xp 00000000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeae12000-7fcaeb011000 ---p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb011000-7fcaeb012000 r--p 00017000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb012000-7fcaeb013000 rw-p 00018000 08:01 9050338 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fcaeb013000-7fcaeb017000 rw-p 00000000 00:00 0 7fcaeb017000-7fcaeb01e000 r-xp 00000000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb01e000-7fcaeb21d000 ---p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21d000-7fcaeb21e000 r--p 00006000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21e000-7fcaeb21f000 rw-p 00007000 08:01 9050343 /lib/x86_64-linux-gnu/librt-2.15.so 7fcaeb21f000-7fcaeb223000 r-xp 00000000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb223000-7fcaeb422000 ---p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb422000-7fcaeb423000 r--p 00003000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb423000-7fcaeb424000 rw-p 00004000 08:01 8661134 /home/biddisco/apps/mpich-3.0.4/lib/libmpl.so.1.0.0 7fcaeb424000-7fcaeb5d9000 r-xp 00000000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb5d9000-7fcaeb7d8000 ---p 001b5000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7d8000-7fcaeb7dc000 r--p 001b4000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7dc000-7fcaeb7de000 rw-p 001b8000 08:01 9050358 /lib/x86_64-linux-gnu/libc-2.15.so 7fcaeb7de000-7fcaeb7e3000 rw-p 00000000 00:00 0 7fcaeb7e3000-7fcaeba03000 r-xp 00000000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaeba03000-7fcaebc03000 ---p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc03000-7fcaebc10000 r--p 00220000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc10000-7fcaebc16000 rw-p 0022d000 08:01 11675463 /home/biddisco/build/mpich-master-v3.0.4-259-gf322ce79/install/lib/libmpich.so.10.0.4 7fcaebc16000-7fcaebc4e000 rw-p 00000000 00:00 0 7fcaebc4e000-7fcaebc70000 r-xp 00000000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fcaebe54000-7fcaebe56000 rw-p 00000000 00:00 0 7fcaebe6d000-7fcaebe70000 rw-p 00000000 00:00 0 7fcaebe70000-7fcaebe71000 r--p 00022000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fcaebe71000-7fcaebe73000 rw-p 00023000 08:01 9050344 /lib/x86_64-linux-gnu/ld-2.15.so 7fff671e5000-7fff67206000 rw-p 00000000 00:00 0 [stack] 7fff673b4000-7fff673b5000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 6 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

1 0

Re: [mpich-discuss] crash on 2^31 size in MPI_Win_allocate_shared(...)
by Weise Steffen 08 Jun '13

08 Jun '13

Dear Jeff, thanks for taking care of the issue. Sure your right about the signed vs. unsigned int stuff but i also tried it with long int : same result. Every integer in my code (memory manager) is long unsigned int, no reason to deal with negative sizes (at least from my perspective). I have an extended version of this example which actually uses the window, sets it and checks it afterwards (but didn't post it to keep the source file small, also the issue is not with that part of the code). All sizes not exactly equal to 2^31 and some multiples of that work very well and "df -h" on /dev/shm clearly shows that it is used correctly. Memory sizes returned by MPI_Win_shared_query also match the requested amount. my installation is in /opt/mpi/ (which would mean i consider MPICH to be THE MPI) ;) I still have to rename my source repo ~/git/openmpi though ;) regards, Steffen Weise First, "long unsigned int window_size=2147483648" is not correct. They type you need to use there is MPI_Aint. The syntax of this function is int MPI_Win_allocate_shared(MPI_Aint size, int disp_unit, MPI_Info info, MPI_Comm comm, void *baseptr, MPI_Win *win) It may be true that "long unsigned int" is safely case to MPI_Aint, but that's a very danger way to write code and it may be broken on some platforms. In any case, everything above 2^31 is probably not okay. Unless absolutely every integer type used in the code paths you are hitting is size_t (or equivalent) and not int, you're going to hit overflow somewhere. Maybe I'm wrong, but you should verify (as a debugging mechanism, not in general) that MPI_Win_allocate_shared is behaving as desired by memset-ing the resulting data (mem) to verify that you're actually getting e.g. 2^34 bytes back. If /dev/shm is 4G, I'm not sure how that's possible but maybe the implementation doesn't use that. I'm going to be on a plane today but I'll run your code on my machine and try to figure out more about how "count-safe" MPI_Win_allocate_shared is. Jeff PS Installing MPICH in ~/git/openmpi is just dirty :-) On Fri, Jun 7, 2013 at 5:50 AM, Weise Steffen <Steffen.Weise(a)iec.tu-freiberg.de<mailto:[email protected]>> wrote: Dear mailing-list, this is my first time posting here. I found that with version 3.0.4 using MPI_Win_allocate_shared i get an error when using a size exactly 2^31 everything below and above is ok. Though i also had the same issue with 2^34. Some kind of division or type conversion seems to be off. (/dev/shm has 4G so it is not a size issue.. i know what those errors look like) I attach my code and the output i get on a linux (debian 6.0) 64 bit machine (same issue on a mac though) . I'll be happy to provide more machine details or everything you guys need to analyse whats going on. with kind regards, Steffen Weise _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Porting MPICH
by Pavan Balaji 07 Jun '13

07 Jun '13

On 06/07/2013 10:10 PM, Jeff Hammond wrote: > I looked into this more thoroughly. The simple solution is to use > "--with-thread-package=no --enable-threads=single" together. The > latter will disable the use of all thread-related functions that lead > to missing symbols due to the former. > > In short, a no-op implementation is not necessary, as I found out > _after_ I had created one. I've committed a patch into mpich/master to throw an error if this happens. -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Porting MPICH
by Jeff Hammond 07 Jun '13

07 Jun '13

I looked into this more thoroughly. The simple solution is to use "--with-thread-package=no --enable-threads=single" together. The latter will disable the use of all thread-related functions that lead to missing symbols due to the former. In short, a no-op implementation is not necessary, as I found out _after_ I had created one. Jeff On Mon, May 20, 2013 at 6:46 AM, jhonatan alves <jhonatanalves1(a)gmail.com> wrote: > Hello, > Today we will try the strategies proposed by you and see how it goes. > > Thank you for helping > > > 2013/5/19 Jeff Hammond <jhammond(a)alcf.anl.gov> >> >> Yeah, I would use the abort strategy to detect if MPICH is using >> thread-related functions in MPI_THREAD_SINGLE (ignoring >> MPICH_ASYNC_PROGRESS=1) and the noop implementation for practical >> purposes. >> >> Jeff >> >> On Sun, May 19, 2013 at 2:49 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: >> > >> > Thanks. Yes, they can be mostly no-ops (except TLS checks which can be >> > any static variable since there's only one thread by definition). >> > Implementing them as "not-implemented" aborts might be OK too. >> > >> > -- Pavan >> > >> > On 05/19/2013 02:43 PM US Central Time, Jeff Hammond wrote: >> >> Presumably those functions can be noops if no threads are going to be >> >> used. Am I wrong? >> >> >> >> It might be worth implementing those functions as stubs that abort >> >> with UNIMPL error and see how far that goes. I'll try to get to this >> >> later today. >> >> >> >> Jeff >> >> >> >> On Sun, May 19, 2013 at 2:36 PM, Pavan Balaji <balaji(a)mcs.anl.gov> >> >> wrote: >> >>> >> >>> On 05/19/2013 02:28 PM US Central Time, jhonatan alves wrote: >> >>>> But i believe that the missing of POSIX >> >>>> threads can be the most trouble part. So we need to port to the >> >>>> thread >> >>>> implementation in EPOS. >> >>> >> >>> Yup, I too believe that'll be the blocker. MPICH supports multiple >> >>> threading packages, but currently requires at least one to function >> >>> correctly: >> >>> >> >>> https://trac.mpich.org/projects/mpich/ticket/231 >> >>> >> >>> It's been a while since I looked into this issue, but I could look >> >>> into >> >>> it if you are running into it for your platform. >> >>> >> >>> -- Pavan >> >>> >> >>> -- >> >>> Pavan Balaji >> >>> http://www.mcs.anl.gov/~balaji >> >>> _______________________________________________ >> >>> discuss mailing list discuss(a)mpich.org >> >>> To manage subscription options or unsubscribe: >> >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> >> >> >> >> >> > >> > -- >> > Pavan Balaji >> > http://www.mcs.anl.gov/~balaji >> >> >> >> -- >> Jeff Hammond >> Argonne Leadership Computing Facility >> University of Chicago Computation Institute >> jhammond(a)alcf.anl.gov / (630) 252-5381 >> http://www.linkedin.com/in/jeffhammond >> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >> ALCF docs: http://www.alcf.anl.gov/user-guides > > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond ALCF docs: http://www.alcf.anl.gov/user-guides

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Re: [mpich-discuss] MPE is available in mpich-3.0.4 ? rlog doesn't work in configure process.
by Jeff Hammond 07 Jun '13

07 Jun '13

Did you read it? It's got the reason that configure is failing pretty clearly stated. You need to debug your configure invocation. Maybe use CC=mpicc etc instead... Jeff Sent from my iPhone On Jun 7, 2013, at 3:04 PM, fernando_luz <fernando_luz(a)tpn.usp.br> wrote: > In attachment. > > Fernando > > On 06/07/2013 04:56 PM, Jeff Hammond wrote: >> please attach config.log. >> >> jeff >> >> On Fri, Jun 7, 2013 at 1:07 PM, fernando_luz <fernando_luz(a)tpn.usp.br> wrote: >>> Hi Rajeev, >>> >>> Thanks for the answers. >>> >>> I get the source code in repository, but I didn't succeed in the compile >>> process. >>> I ran the autogen.sh and after this I tried to configure my installation and >>> I received the following error message. >>> >>> >>> fernando_luz@TPN000300:~/git/mpe$ ./configure >>> --prefix=/home/fernando_luz/usr/mpe >>> --with-mpicc=/home/fernando_luz/usr/mpich/bin/mpicc >>> --with-mpilibs=/home/fernando_luz/usr/mpich/lib/ >>> --with-mpiinc=/home/fernando_luz/usr/mpich/include/ >>> Configuring MPE Profiling System with '--prefix=/home/fernando_luz/usr/mpe' >>> '--with-mpicc=/home/fernando_luz/usr/mpich/bin/mpicc' >>> '--with-mpilibs=/home/fernando_luz/usr/mpich/lib/' >>> '--with-mpiinc=/home/fernando_luz/usr/mpich/include/' >>> 'MPI_CC=/home/fernando_luz/usr/mpich/bin/mpicc' >>> 'MPI_INC=/home/fernando_luz/usr/mpich/include' >>> 'MPI_LIBS=/home/fernando_luz/usr/mpich/lib' >>> checking for current directory name... /home/fernando_luz/git/mpe >>> checking gnumake... yes using --no-print-directory >>> checking BSD 4.4 make... no - whew >>> checking OSF V3 make... no >>> checking for virtual path format... VPATH >>> User supplied MPI implmentation (Good Luck!) >>> checking for leftover Makefiles in subpackages ... none >>> checking for gcc... cc >>> checking whether the C compiler works... yes >>> checking for C compiler default output file name... a.out >>> checking for suffix of executables... >>> checking whether we are cross compiling... no >>> checking for suffix of object files... o >>> checking whether we are using the GNU C compiler... yes >>> checking whether cc accepts -g... yes >>> checking for cc option to accept ISO C89... none needed >>> checking whether MPI_CC has been set ... >>> /home/fernando_luz/usr/mpich/bin/mpicc >>> checking whether we are using the GNU Fortran 77 compiler... no >>> checking whether f77 accepts -g... no >>> checking whether MPI_F77 has been set ... f77 >>> checking for the linkage of the supplied MPI C definitions ... no >>> configure: error: Cannot link with basic MPI C program! >>> Check your MPI include paths, MPI libraries and MPI CC compiler >>> >>> Where /home/fernando_luz/usr/mpich/ is my mpi installation (MPICH-3.0.4). >>> >>> I prefer to use the mpe in repository because in the site, the last version >>> was dated in 2010 and in the git repository the last commit was in 2012. >>> >>> Regards >>> >>> Fernando >>> >>> >>> >>> On 06/04/2013 03:05 PM, Rajeev Thakur wrote: >>>> It can be downloaded from >>>> http://www.mcs.anl.gov/research/projects/perfvis/download/index.htm. >>>> >>>> The source repository is at http://git.mpich.org/mpe.git/ >>>> >>>> Rajeev >>>> >>>> On Jun 4, 2013, at 12:48 PM, Jeff Hammond wrote: >>>> >>>>> MPE isn't actively developed and should sit strictly on top of any MPI >>>>> implementation so you can just grab MPE from an older release of >>>>> MPICH. >>>>> >>>>> My guess is that MPE will be a standalone download at some point in the >>>>> future. >>>>> >>>>> Jeff >>>>> >>>>> On Tue, Jun 4, 2013 at 10:59 AM, fernando_luz <fernando_luz(a)tpn.usp.br> >>>>> wrote: >>>>>> Hi, >>>>>> >>>>>> I didn't find the MPE source in mpich-3.0.4 package. Where I can >>>>>> download >>>>>> the source? It is still compatible with mpich? >>>>>> >>>>>> And I tried to install the logging support available in this release, >>>>>> but my >>>>>> try didn't was successful. I received the follow error: >>>>>> >>>>>> /home/fernando_luz/software/mpich-3.0.4/src/util/logging/rlog/configure: >>>>>> line 3694: PAC_CC_SUBDIR_SHLIBS: command not found >>>>>> configure: creating ./config.status >>>>>> config.status: error: cannot find input file: `Makefile.in' >>>>>> configure: error: src/util/logging/rlog configure failed >>>>>> >>>>>> I attached the c.txt file used in the configuration. >>>>>> >>>>>> Regards >>>>>> >>>>>> Fernando >>>>>> >>>>>> _______________________________________________ >>>>>> discuss mailing list discuss(a)mpich.org >>>>>> To manage subscription options or unsubscribe: >>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>>> >>>>> -- >>>>> Jeff Hammond >>>>> Argonne Leadership Computing Facility >>>>> University of Chicago Computation Institute >>>>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>>>> http://www.linkedin.com/in/jeffhammond >>>>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>>>> ALCF docs: http://www.alcf.anl.gov/user-guides >>>>> _______________________________________________ >>>>> 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 >> >> > > <config.log> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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