Dear All,
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 Dec 26 2012 - 10:30:02 PST
