i think you need to ask people about the method you're using, not the
program. Since email subject lines are so important, send a new email with
a subject related to the method you're using and the error you get. With
your current subject, only people that know about LES will read your email
in detail, and your problem seems to actually relate to PIMD.
the LES test case (it won't test PIMD in the example below) tells you that
you need to use a different number of processors to have it work. You could
try doing that- but again, it's not the PIMD test.
On Wed, Jan 2, 2013 at 11:08 AM, Kirill Nuzhdin <knuzhdin.nd.edu> wrote:
> Does anyone know if I'm using sander.LES.MPI in a correct way?
> Are there any reasonable examples? The only example of Malonaldehyde
> from the Amber12 manual (and the test suite) is somewhat brief and useless.
>
> As for test cases, I found logs for tests, where it looks like LES.MPI
> tests are skipped:
> =============================
> export TESTsanderLES=/opt/crc/amber/amber12/intel/bin/sander.LES.MPI;
> make -k test.sander.LES
> make[3]: Entering directory
> `/afs/crc.nd.edu/x86_64_linux/amber/amber12/intel/test'
> cd LES_noPME && ./Run.LESmd
> SANDER: LES MD gas phase
> DO_PARALLEL set to mpirun -np 16
> too many processors for this test, exiting (Max = 12)
> ============================================================
> cd LES_noPME && ./Run.LESmd.rdiel
> SANDER: LES MD gas phase rdiel
> DO_PARALLEL set to mpirun -np 16
> too many processors for this test, exiting (Max = 12)
> =============================
>
>
> On 12/26/2012 1:39 PM, Carlos Simmerling wrote:
> > Did the test case pass?
> > On Dec 26, 2012 12:27 PM, "Kirill Nuzhdin" <knuzhdin.nd.edu> wrote:
> >
> >> trying to run sander.LES.MPI like that:
> >> mpiexec -n 4 $AMBERHOME/bin/sander.LES.MPI -ng 4 -groupfile
> >> gf_Hqspcfw.pimd > sander_Hqspcfw.pimd.out
> >>
> >> where
> >>
> >>
> >> gf_Hqspcfw.pimd:
> >> =============================
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.1 -o
> >> bead.pimd1.out -r bead.pimd1.rst -x bead.pimd1.crd -v bead.pimd1.vel
> >> -inf bead.pimd1.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.2 -o
> >> bead.pimd2.out -r bead.pimd2.rst -x bead.pimd2.crd -v bead.pimd2.vel
> >> -inf bead.pimd2.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.3 -o
> >> bead.pimd3.out -r bead.pimd3.rst -x bead.pimd3.crd -v bead.pimd3.vel
> >> -inf bead.pimd3.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.4 -o
> >> bead.pimd4.out -r bead.pimd4.rst -x bead.pimd4.crd -v bead.pimd4.vel
> >> -inf bead.pimd4.info -pimdout rpmd.pimd.out
> >> =============================
> >>
> >>
> >> Hqspcfw.pimd.in:
> >> =============================
> >> &cntrl
> >> ipimd = 4
> >> ntx = 1, irest = 0
> >> ntt = 0
> >> jfastw = 4
> >> nscm = 0
> >> temp0 = 300.0, temp0les = -1.
> >> dt = 0.0002, nstlim = 10
> >> cut = 7.0
> >> ntpr = 1, ntwr = 5, ntwx = 1, ntwv = 1
> >> /
> >> =============================
> >>
> >>
> >> non-MPI, LES version running with Hqspcfw.pimd.in, Hqspcfw.pimd.prmtop
> >> and spcfw.pimd.rst.* is fine!
> >>
> >> while sander.LES.MPI (as soon as any of the four tasks from the group
> >> file is done) is crashing with the following error:
> >>
> >> =============================
> >> *** glibc detected *** /opt/crc/amber/amber12/intel/bin/sander.LES.MPI:
> >> munmap_chunk(): invalid pointer: 0x00000000206132b0 ***
> >> ======= Backtrace: =========
> >> /lib64/libc.so.6(cfree+0x166)[0x31060729d6]
> >> /afs/
> >>
> crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for__free_vm+0x1b)[0x2b0a7266249b]
> >>
> >> /afs/
> crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for__deallocate_lub+0x13a)[0x2b0a726309da]
> >>
> >> /afs/
> crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for_close+0x448)[0x2b0a72608b08]
> >>
> >>
> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(close_dump_files_+0x122)[0x588ad2]
> >>
> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(sander_+0xa961)[0x506ac5]
> >> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(MAIN__+0x1c4b)[0x4fc0cb]
> >> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(main+0x3c)[0x46cbec]
> >> /lib64/libc.so.6(__libc_start_main+0xf4)[0x310601d994]
> >> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI[0x46caf9]
> >> =============================
> >>
> >> how to avoid that?
> >>
> >> Thank you!
>
> --
> Best regards,
> Kirill Nuzhdin
>
>
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Received on Wed Jan 02 2013 - 09:30:03 PST
