[gmx-developers] gromacs 4.5 git + openmm-2.0 + OpenCL
Alexey Shvetsov
alexxyum at gmail.com
Mon Aug 16 21:28:56 CEST 2010
Hi all!
Recently i tryed to build gromacs 4.5 + openmm with opencl support.
Seems it builds fine. Also i can do test run ( for example speptide in
water box) but mdrun always segfaults when it finishing. right after
writing last frame of trajectory.
I get this in backtrace
starting mdrun 'Protein in water'
5000 steps, 10.0 ps.
step 4900, remaining runtime: 3 s
Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.1#
step 5000, remaining runtime: 0 s *** glibc detected ***
/home/alexxy/Soft/openmm/bin/mdrun-gpu: free(): invalid pointer:
0x000000000137ed78 ***
======= Backtrace: =========
/lib/libc.so.6(+0x71c45)[0x2aaaac99ec45]
/lib/libc.so.6(cfree+0x6c)[0x2aaaac9a3b3c]
/home/alexxy/Soft/openmm/lib/plugins/libOpenMMOpenCL.so(_ZN6OpenMM34OpenCLCalcHarmonicAngleForceKernelD1Ev+0x5c)[0x2aaaadc13d9c]
/home/alexxy/Soft/openmm/lib/plugins/libOpenMMOpenCL.so(_ZN6OpenMM34OpenCLCalcHarmonicAngleForceKernelD0Ev+0x9)[0x2aaaadc13ea9]
/home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM22HarmonicAngleForceImplD1Ev+0x1b)[0x2aaaaaf51d1b]
/home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM22HarmonicAngleForceImplD0Ev+0x9)[0x2aaaaaf51d59]
/home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM11ContextImplD1Ev+0x37)[0x2aaaaaf2c607]
/home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM7ContextD2Ev+0x21)[0x2aaaaaf41631]
/home/alexxy/Soft/openmm/bin/mdrun-gpu(openmm_cleanup+0xed)[0x531ebd]
/home/alexxy/Soft/openmm/bin/mdrun-gpu(do_md_openmm+0x1480)[0x443270]
/home/alexxy/Soft/openmm/bin/mdrun-gpu(mdrunner+0xbe3)[0x422713]
/home/alexxy/Soft/openmm/bin/mdrun-gpu(main+0x1148)[0x43f278]
/lib/libc.so.6(__libc_start_main+0xfd)[0x2aaaac94bb3d]
/home/alexxy/Soft/openmm/bin/mdrun-gpu[0x41acc9]
======= Memory map: ========
00400000-00719000 r-xp 00000000 fe:09 1284469
/home/alexxy/Soft/openmm/bin/mdrun-gpu
00919000-0091a000 r--p 00319000 fe:09 1284469
/home/alexxy/Soft/openmm/bin/mdrun-gpu
0091a000-0091c000 rw-p 0031a000 fe:09 1284469
/home/alexxy/Soft/openmm/bin/mdrun-gpu
0091c000-019a1000 rw-p 00000000 00:00 0 [heap]
2aaaaaaab000-2aaaaaac9000 r-xp 00000000 fe:02 9726
/lib64/ld-2.11.2.so
2aaaaaac9000-2aaaaaaca000 r-xp 00000000 00:00 0 [vdso]
2aaaaaaca000-2aaaaaacc000 rw-p 00000000 00:00 0
2aaaaaacd000-2aaaaab1d000 rw-p 00000000 00:00 0
2aaaaacc8000-2aaaaacc9000 r--p 0001d000 fe:02 9726
/lib64/ld-2.11.2.so
2aaaaacc9000-2aaaaacca000 rw-p 0001e000 fe:02 9726
/lib64/ld-2.11.2.so
2aaaaacca000-2aaaaaccb000 rw-p 00000000 00:00 0
2aaaaaccb000-2aaaaaccd000 r-xp 00000000 fe:02 9731
/lib64/libdl-2.11.2.so
2aaaaaccd000-2aaaaaecd000 ---p 00002000 fe:02 9731
/lib64/libdl-2.11.2.so
2aaaaaecd000-2aaaaaece000 r--p 00002000 fe:02 9731
/lib64/libdl-2.11.2.so
2aaaaaece000-2aaaaaecf000 rw-p 00003000 fe:02 9731
/lib64/libdl-2.11.2.so
2aaaaaecf000-2aaaaaed0000 rw-p 00000000 00:00 0
2aaaaaed0000-2aaaab013000 r-xp 00000000 fe:09 1155278
/home/alexxy/Soft/openmm/lib/libOpenMM.so
2aaaab013000-2aaaab213000 ---p 00143000 fe:09 1155278
/home/alexxy/Soft/openmm/lib/libOpenMM.so
2aaaab213000-2aaaab219000 r--p 00143000 fe:09 1155278
/home/alexxy/Soft/openmm/lib/libOpenMM.so
2aaaab219000-2aaaab21c000 rw-p 00149000 fe:09 1155278
/home/alexxy/Soft/openmm/lib/libOpenMM.so
2aaaab21c000-2aaaab21d000 rw-p 00000000 00:00 0
2aaaab21d000-2aaaab29d000 r-xp 00000000 fe:02 11328
/lib64/libm-2.11.2.so
2aaaab29d000-2aaaab49d000 ---p 00080000 fe:02 11328
/lib64/libm-2.11.2.so
2aaaab49d000-2aaaab49e000 r--p 00080000 fe:02 11328
/lib64/libm-2.11.2.so
2aaaab49e000-2aaaab49f000 rw-p 00081000 fe:02 11328
/lib64/libm-2.11.2.so
2aaaab49f000-2aaaab5e7000 r-xp 00000000 fe:04 2483
/usr/lib64/libxml2.so.2.7.7
2aaaab5e7000-2aaaab7e6000 ---p 00148000 fe:04 2483
/usr/lib64/libxml2.so.2.7.7
2aaaab7e6000-2aaaab7ee000 r--p 00147000 fe:04 2483
/usr/lib64/libxml2.so.2.7.7
2aaaab7ee000-2aaaab7f0000 rw-p 0014f000 fe:04 2483
/usr/lib64/libxml2.so.2.7.7
2aaaab7f0000-2aaaab7f2000 rw-p 00000000 00:00 0
2aaaab7f2000-2aaaab823000 r-xp 00000000 fe:03 4651
/opt/cuda/lib64/libcudart.so.3.1.9
2aaaab823000-2aaaaba23000 ---p 00031000 fe:03 4651
/opt/cuda/lib64/libcudart.so.3.1.9
2aaaaba23000-2aaaaba24000 r--p 00031000 fe:03 4651
/opt/cuda/lib64/libcudart.so.3.1.9
2aaaaba24000-2aaaaba25000 rw-p 00032000 fe:03 4651
/opt/cuda/lib64/libcudart.so.3.1.9
2aaaaba25000-2aaaac136000 r-xp 00000000 fe:04 766197
/usr/lib64/libcuda.so.256.44
2aaaac136000-2aaaac335000 ---p 00711000 fe:04 766197
/usr/lib64/libcuda.so.256.44
2aaaac335000-2aaaac3e9000 rw-p 00710000 fe:04 766197
/usr/lib64/libcuda.so.256.44
2aaaac3e9000-2aaaac40d000 rw-p 00000000 00:00 0
2aaaac40d000-2aaaac4f8000 r-xp 00000000 fe:04 713749
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libstdc++.so.6.0.14
2aaaac4f8000-2aaaac6f7000 ---p 000eb000 fe:04 713749
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libstdc++.so.6.0.14
2aaaac6f7000-2aaaac6ff000 r--p 000ea000 fe:04 713749
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libstdc++.so.6.0.14
2aaaac6ff000-2aaaac701000 rw-p 000f2000 fe:04 713749
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libstdc++.so.6.0.14
2aaaac701000-2aaaac717000 rw-p 00000000 00:00 0
2aaaac717000-2aaaac72c000 r-xp 00000000 fe:04 713750
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libgcc_s.so.1
2aaaac72c000-2aaaac92b000 ---p 00015000 fe:04 713750
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libgcc_s.so.1
2aaaac92b000-2aaaac92c000 r--p 00014000 fe:04 713750
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libgcc_s.so.1
2aaaac92c000-2aaaac92d000 rw-p 00015000 fe:04 713750
/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libgcc_s.so.1
2aaaac92d000-2aaaaca7f000 r-xp 00000000 fe:02 11342
/lib64/libc-2.11.2.so
2aaaaca7f000-2aaaacc7e000 ---p 00152000 fe:02 11342
/lib64/libc-2.11.2.so
2aaaacc7e000-2aaaacc82000 r--p 00151000 fe:02 11342
/lib64/libc-2.11.2.so
2aaaacc82000-2aaaacc83000 rw-p 00155000 fe:02 11342
/lib64/libc-2.11.2.so
2aaaacc83000-2aaaacc88000 rw-p 00000000 00:00 0
2aaaacc88000-2aaaacc9e000 r-xp 00000000 fe:02 11325
/lib64/libpthread-2.11.2.so
2aaaacc9e000-2aaaace9e000 ---p 00016000 fe:02 11325
/lib64/libpthread-2.11.2.so
2aaaace9e000-2aaaace9f000 r--p 00016000 fe:02 11325
/lib64/libpthread-2.11.2.so
Program received signal SIGABRT, Aborted.
0x00002aaaac95f405 in *__GI_raise (sig=<value optimized out>) at
../nptl/sysdeps/unix/sysv/linux/raise.c:64
64 ../nptl/sysdeps/unix/sysv/linux/raise.c: Нет такого файла или каталога.
in ../nptl/sysdeps/unix/sysv/linux/raise.c
(gdb) bt
#0 0x00002aaaac95f405 in *__GI_raise (sig=<value optimized out>) at
../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00002aaaac960705 in *__GI_abort () at abort.c:92
#2 0x00002aaaac9997c2 in __libc_message (do_abort=2,
fmt=0x2aaaaca4ad08 "*** glibc detected *** %s: %s: 0x%s ***\n") at
../sysdeps/unix/sysv/linux/libc_fatal.c:186
#3 0x00002aaaac99ec45 in malloc_printerr (action=3,
str=0x2aaaaca47f81 "free(): invalid pointer", ptr=<value optimized
out>) at malloc.c:6267
#4 0x00002aaaac9a3b3c in *__GI___libc_free (mem=<value optimized
out>) at malloc.c:3739
#5 0x00002aaaadc13d9c in ~OpenCLCalcHarmonicAngleForceKernel
(this=0x137e880, __in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/platforms/opencl/src/OpenCLKernels.cpp:452
#6 0x00002aaaadc13ea9 in ~OpenCLCalcHarmonicAngleForceKernel
(this=0x137e880, __in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/platforms/opencl/src/OpenCLKernels.cpp:455
#7 0x00002aaaaaf51d1b in ~HarmonicAngleForceImpl (this=0xa92b90,
__in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/HarmonicAngleForceImpl.cpp:44
#8 0x00002aaaaaf51d59 in ~HarmonicAngleForceImpl (this=0xa92b90,
__in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/HarmonicAngleForceImpl.cpp:45
#9 0x00002aaaaaf2c607 in ~ContextImpl (this=0xc2b380,
__in_chrg=<value optimized out>) at
/home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/ContextImpl.cpp:87
#10 0x00002aaaaaf41631 in ~Context (this=0xc2b340, __in_chrg=<value
optimized out>) at
/home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/Context.cpp:52
#11 0x0000000000531ebd in openmm_cleanup (fplog=0x9206d0,
data=0x14477f0) at
/home/alexxy/Src/gromacs/src/kernel/openmm_wrapper.cpp:1362
#12 0x0000000000443270 in do_md_openmm (fplog=0x9206d0, cr=<value
optimized out>, nfile=27, fnm=0x7fffffffbea0, oenv=<value optimized
out>, bVerbose=1, bCompact=1,
nstglobalcomm=-1, vsite=0x0, constr=0x9bfe60, stepout=100,
ir=0x9212a0, top_global=0x920d90, fcd=0x94ac70, state_global=0x921830,
mdatoms=0x98ed30, nrnb=0x94b160,
wcycle=0x9211d0, ed=0x0, fr=0x94b7d0, repl_ex_nst=0,
repl_ex_seed=-1, cpt_period=15, max_hours=-1,
deviceOptions=0x7fffffffd27b "OpenMM:platform=OpenCL,memtest=15",
Flags=7168, runtime=0x7fffffffad70) at
/home/alexxy/Src/gromacs/src/kernel/md_openmm.c:675
#13 0x0000000000422713 in mdrunner (nthreads_requested=<value
optimized out>, fplog=0x9206d0, cr=0x91f6f0, nfile=27,
fnm=0x7fffffffbea0, oenv=0x91fd10, bVerbose=1, bCompact=1,
nstglobalcomm=-1, ddxyz=0x7fffffffca80, dd_node_order=1, rdd=0,
rconstr=0, dddlb_opt=0x6a26fd "auto", dlb_scale=0.80000000000000004,
ddcsx=0x0, ddcsy=0x0, ddcsz=0x0,
nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0,
repl_ex_seed=-1, pforce=0, cpt_period=15, max_hours=-1,
deviceOptions=0x7fffffffd27b "OpenMM:platform=OpenCL,memtest=15",
Flags=<value optimized out>) at
/home/alexxy/Src/gromacs/src/kernel/runner.c:789
#14 0x000000000043f278 in main (argc=6, argv=0x7fffffffcc68) at
/home/alexxy/Src/gromacs/src/kernel/mdrun.c:635
(gdb) up
#1 0x00002aaaac960705 in *__GI_abort () at abort.c:92
92 abort.c: Нет такого файла или каталога.
in abort.c
(gdb) up
#2 0x00002aaaac9997c2 in __libc_message (do_abort=2,
fmt=0x2aaaaca4ad08 "*** glibc detected *** %s: %s: 0x%s ***\n") at
../sysdeps/unix/sysv/linux/libc_fatal.c:186
186 ../sysdeps/unix/sysv/linux/libc_fatal.c: Нет такого файла или каталога.
in ../sysdeps/unix/sysv/linux/libc_fatal.c
(gdb) up
#3 0x00002aaaac99ec45 in malloc_printerr (action=3,
str=0x2aaaaca47f81 "free(): invalid pointer", ptr=<value optimized
out>) at malloc.c:6267
6267 malloc.c: Нет такого файла или каталога.
in malloc.c
(gdb) up
#4 0x00002aaaac9a3b3c in *__GI___libc_free (mem=<value optimized
out>) at malloc.c:3739
3739 in malloc.c
(gdb) up
#5 0x00002aaaadc13d9c in ~OpenCLCalcHarmonicAngleForceKernel
(this=0x137e880, __in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/platforms/opencl/src/OpenCLKernels.cpp:452
452 delete params;
(gdb) up
#6 0x00002aaaadc13ea9 in ~OpenCLCalcHarmonicAngleForceKernel
(this=0x137e880, __in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/platforms/opencl/src/OpenCLKernels.cpp:455
455 }
(gdb) up
#7 0x00002aaaaaf51d1b in ~HarmonicAngleForceImpl (this=0xa92b90,
__in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/HarmonicAngleForceImpl.cpp:44
44 HarmonicAngleForceImpl::~HarmonicAngleForceImpl() {
(gdb) up
#8 0x00002aaaaaf51d59 in ~HarmonicAngleForceImpl (this=0xa92b90,
__in_chrg=<value optimized out>)
at /home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/HarmonicAngleForceImpl.cpp:45
45 }
(gdb) up
#9 0x00002aaaaaf2c607 in ~ContextImpl (this=0xc2b380,
__in_chrg=<value optimized out>) at
/home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/ContextImpl.cpp:87
87 delete forceImpls[i];
(gdb) up
#10 0x00002aaaaaf41631 in ~Context (this=0xc2b340, __in_chrg=<value
optimized out>) at
/home/alexxy/Src/OpenMM2.0-Source/src/openmmapi/src/Context.cpp:52
52 delete impl;
(gdb) up
#11 0x0000000000531ebd in openmm_cleanup (fplog=0x9206d0,
data=0x14477f0) at
/home/alexxy/Src/gromacs/src/kernel/openmm_wrapper.cpp:1362
1362 delete d->context;
(gdb) up
#12 0x0000000000443270 in do_md_openmm (fplog=0x9206d0, cr=<value
optimized out>, nfile=27, fnm=0x7fffffffbea0, oenv=<value optimized
out>, bVerbose=1, bCompact=1,
nstglobalcomm=-1, vsite=0x0, constr=0x9bfe60, stepout=100,
ir=0x9212a0, top_global=0x920d90, fcd=0x94ac70, state_global=0x921830,
mdatoms=0x98ed30, nrnb=0x94b160,
wcycle=0x9211d0, ed=0x0, fr=0x94b7d0, repl_ex_nst=0,
repl_ex_seed=-1, cpt_period=15, max_hours=-1,
deviceOptions=0x7fffffffd27b "OpenMM:platform=OpenCL,memtest=15",
Flags=7168, runtime=0x7fffffffad70) at
/home/alexxy/Src/gromacs/src/kernel/md_openmm.c:675
675 openmm_cleanup(fplog, openmmData);
(gdb) up
#13 0x0000000000422713 in mdrunner (nthreads_requested=<value
optimized out>, fplog=0x9206d0, cr=0x91f6f0, nfile=27,
fnm=0x7fffffffbea0, oenv=0x91fd10, bVerbose=1, bCompact=1,
nstglobalcomm=-1, ddxyz=0x7fffffffca80, dd_node_order=1, rdd=0,
rconstr=0, dddlb_opt=0x6a26fd "auto", dlb_scale=0.80000000000000004,
ddcsx=0x0, ddcsy=0x0, ddcsz=0x0,
nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0,
repl_ex_seed=-1, pforce=0, cpt_period=15, max_hours=-1,
deviceOptions=0x7fffffffd27b "OpenMM:platform=OpenCL,memtest=15",
Flags=<value optimized out>) at
/home/alexxy/Src/gromacs/src/kernel/runner.c:789
789 integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
(gdb) up
#14 0x000000000043f278 in main (argc=6, argv=0x7fffffffcc68) at
/home/alexxy/Src/gromacs/src/kernel/mdrun.c:635
635 rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
--
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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