starting mdrun 'Protein'
1000 steps, 2.0 ps.
Error: too many resources requested for launch launching kernel kCalculateCDLJObcGbsaN2Forces1
how solve this problem?
Thank you very very much!
Romica Sandu
Error: too many resources requested for launc
-
Romica Sandu
- Posts: 12
- Joined: Tue Sep 30, 2008 11:41 am
-
Romica Sandu
- Posts: 12
- Joined: Tue Sep 30, 2008 11:41 am
RE: Error: too many resources requested for launc
OpenMM Platform: Cuda
starting mdrun 'Protein'
1000 steps, 2.0 ps.
Error: too many resources requested for launch launching kernel
kCalculateCDLJObcGbsaN2Forces1
starting mdrun 'Protein'
1000 steps, 2.0 ps.
Error: too many resources requested for launch launching kernel
kCalculateCDLJObcGbsaN2Forces1
-
Mark Friedrichs
- Posts: 32
- Joined: Fri Jun 09, 2006 11:23 am
RE: Error: too many resources requested for launc
This indicates a problem w/ the number of registers, shared memory, threads, ... being used on the NVIDIA board. How big is the system you are trying to simulate? If you send me your tpr file (friedrim@stanford.edu), I could run it here and see if I can reproduce the problem.
RE: Error: too many resources requested for launc
Dear Romica/Mark,
I too get this message, using the precompiled preview 3 version of Gromacs/OpenMM, when attempting to simulate the villin headpiece. The system ran fine using the preview 2 version.
Thanks in advance
I too get this message, using the precompiled preview 3 version of Gromacs/OpenMM, when attempting to simulate the villin headpiece. The system ran fine using the preview 2 version.
Thanks in advance
-
Romica Sandu
- Posts: 12
- Joined: Tue Sep 30, 2008 11:41 am
RE: Error: too many resources requested for launc
Without GBSA the simulation run well and in the precompiled preview 3 version of Gromacs/OpenMM.
I had error with GBSA. I sent the file .tpr to Mark Friedrichs
Thanks you very much.
I had error with GBSA. I sent the file .tpr to Mark Friedrichs
Thanks you very much.
-
Mark Friedrichs
- Posts: 32
- Joined: Fri Jun 09, 2006 11:23 am
RE: Error: too many resources requested for launc
Hi Romica.
I was able to run the reaper.tpr here on a NVIDIA GTX280 w/o problems. I emailed you a tgz file w/ the results; the file 'stdout_err' in the tgz contains the output to stdout & stderr for the run. The GTS250 should be able to handle the system. We do not have a board of that type here so I cannot directly check. I had a problem like this several months ago, and the solution was to change one of the NVIDIA compiler flags. So I regenerated the libs with this change and posted the libs at http://www.stanford.edu/~friedrim/ Please replace the ones you downloaded earlier w/ these (libOpenMMCuda.so and libOpenMM.so) and try again -- let us know if it is still not working.
Mark
I was able to run the reaper.tpr here on a NVIDIA GTX280 w/o problems. I emailed you a tgz file w/ the results; the file 'stdout_err' in the tgz contains the output to stdout & stderr for the run. The GTS250 should be able to handle the system. We do not have a board of that type here so I cannot directly check. I had a problem like this several months ago, and the solution was to change one of the NVIDIA compiler flags. So I regenerated the libs with this change and posted the libs at http://www.stanford.edu/~friedrim/ Please replace the ones you downloaded earlier w/ these (libOpenMMCuda.so and libOpenMM.so) and try again -- let us know if it is still not working.
Mark
-
Romica Sandu
- Posts: 12
- Joined: Tue Sep 30, 2008 11:41 am
RE: Error: too many resources requested for launc
"Pick Up the Pieces"
(http://www.youtube.com/watch?v=76kd984x ... re=related)
I think that I installed something astray and not go.
I'm going to reinstall later the version pr3.
I have ubuntu 9.04 32 with gromacs 4.0.5.1 installed
cuda it is in usr/local/cuda
mdrun 4.0.5.1, mdrun-openmm pr3 in /usr/bin
top it is in /usr/share/gromacs/top
I will try to clarify my some things, maybe someone can help me:
cuda, libcudart.so2.2, mdrun 4.0.5.1, mdrun-openmm pr3,libOpenMM.so,
libOpenMMCuda.so, gbsaObc, plugin libraries and others, in what directory
and what is the command for path for each?
Thank you very much!
Romica
(http://www.youtube.com/watch?v=76kd984x ... re=related)
I think that I installed something astray and not go.
I'm going to reinstall later the version pr3.
I have ubuntu 9.04 32 with gromacs 4.0.5.1 installed
cuda it is in usr/local/cuda
mdrun 4.0.5.1, mdrun-openmm pr3 in /usr/bin
top it is in /usr/share/gromacs/top
I will try to clarify my some things, maybe someone can help me:
cuda, libcudart.so2.2, mdrun 4.0.5.1, mdrun-openmm pr3,libOpenMM.so,
libOpenMMCuda.so, gbsaObc, plugin libraries and others, in what directory
and what is the command for path for each?
Thank you very much!
Romica
-
Mark Friedrichs
- Posts: 32
- Joined: Fri Jun 09, 2006 11:23 am
RE: Error: too many resources requested for launc
The location of the libraries is to some extent arbitrary. The important point is to have the environment variables set to the location of the files -- typically
libcudart.so2.2 is in /usr/local/cuda/lib
libOpenMM.so is in /usr/local/openmm/lib and
libOpenMMCuda.so is in /usr/local/openmm/lib/plugins
If you use the above setup, then the environment variable. 'LD_LIBRARY_PATH' should include the paths "/usr/local/cuda/lib:/usr/local/openmm/lib" and the environment variable, 'OPENMM_PLUGIN_DIR' should include "/usr/local/openmm/lib/plugins"
libcudart.so2.2 is in /usr/local/cuda/lib
libOpenMM.so is in /usr/local/openmm/lib and
libOpenMMCuda.so is in /usr/local/openmm/lib/plugins
If you use the above setup, then the environment variable. 'LD_LIBRARY_PATH' should include the paths "/usr/local/cuda/lib:/usr/local/openmm/lib" and the environment variable, 'OPENMM_PLUGIN_DIR' should include "/usr/local/openmm/lib/plugins"
-
Romica Sandu
- Posts: 12
- Joined: Tue Sep 30, 2008 11:41 am
RE: Error: too many resources requested for launc
Sorry, I need further advice from your.
I could not obtain a trajectory of 100 ns with OpenMM-pr2.
After 7ns my simulation stops with the same message that appears
in OpenMM-pr3 with no running.
Here are portions of md.log:
<
Log file opened on Sat Jun 6 13:59:27 2009
Host: paco pid: 4380 nodeid: 0 nnodes: 1
The Gromacs distribution was built Fri Feb 6 09:33:59 PST 2009 by
cmbruns@cmbruns.stanford.edu (Linux 2.6.18-92.1.22.el5 i686)
G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
VERSION 4.0.3_pre (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
mdrun_openmm (-:
.
.
.
andersen_seed = 815131
rlist = 100
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 100
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 100
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-05
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
.
.
.
qm_opts:
ngQM = 0
nstvmdout = 0
vmdSocketNumber = 0
blockUntilVmdConnected = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 100 Coulomb: 100 LJ: 100
System total charge: 6.000
Generated table with 50500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 50500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 50500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 557
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest
There are: 1098 Atoms
Successfully loaded plugin /usr/lib/openmm/libOpenMM.so
Successfully loaded plugin /usr/lib/openmm/libOpenMMCuda.so
agb parameter file line=<> is being skipped.
agb parameter file line=<> is being skipped.
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 5.55e-06
Initial temperature: 295.765 K
Started mdrun on node 0 Sat Jun 6 13:59:28 2009
Step Time Lambda
1 0.00200 0.00000
Step Time Lambda
1000 2.00000 0.00000
Step Time Lambda
.
.
.
Step Time Lambda
7665000 15330.00098 0.00000
Step Time Lambda
7666000 15332.00098 0.00000
Step Time Lambda
7667000 15334.00098 0.00000
Step Time Lambda
7668000 15336.00098 0.00000
here stops in md.log
----------------------------
and from terminal after stops:
Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 4.0.5 (single precision)
Note: tpx file_version 58, software version 59
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
directory: /usr/lib/openmm
OpenMM Platform: Cuda
starting mdrun 'Protein'
35000000 steps, 70000.0 ps.
Error: unspecified launch failure launching kernel kCalculateObcGbsaForces2
*** glibc detected *** mdrun_openmm: double free or corruption (fasttop): 0x098409e0 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0xb7a08604]
/lib/tls/i686/cmov/libc.so.6(cfree+0x96)[0xb7a0a5b6]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7beb231]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0xb7bc79fd]
libOpenMM.so[0xb7fcf1ea]
/lib/tls/i686/cmov/libc.so.6(__cxa_finalize+0xc1)[0xb79c7f51]
libOpenMM.so[0xb7f9b804]
libOpenMM.so[0xb7fd986c]
/lib/ld-linux.so.2[0xb7fffa73]
/lib/tls/i686/cmov/libc.so.6(exit+0x89)[0xb79c7bb9]
/usr/lib/openmm/libOpenMMCuda.so[0xb764911d]
/usr/lib/openmm/libOpenMMCuda.so[0xb7626e9e]
libOpenMM.so(_ZN6OpenMM21HarmonicBondForceImpl10calcForcesERNS_17OpenMMContextImplERNS_6StreamE+0x59)[0xb7faa3e9]
libOpenMM.so(_ZN6OpenMM17OpenMMContextImpl10calcForcesEv+0x7d)[0xb7fa17dd]
libOpenMM.so(_ZN6OpenMM18LangevinIntegrator4stepEi+0x43)[0xb7fa62c3]
mdrun_openmm[0x8060f7e]
mdrun_openmm[0x805b50d]
mdrun_openmm[0x8059d6f]
mdrun_openmm[0x805cb46]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe5)[0xb79af775]
mdrun_openmm(__gxx_personality_v0+0x141)[0x804bb71]
======= Memory map: ========
08048000-082a5000 r-xp 00000000 08:11 4743340 /usr/bin/mdrun_openmm
082a5000-082ad000 rwxp 0025d000 08:11 4743340 /usr/bin/mdrun_openmm
082ad000-082b3000 rwxp 082ad000 00:00 0
09777000-09a63000 rwxp 09777000 00:00 0 [heap]
b29ce000-b67a5000 rwxp b29ce000 00:00 0
b67a5000-b68a5000 rwxs 10408000 00:0f 8256 /dev/nvidia0
b68a5000-b69a5000 rwxs 10b03000 00:0f 8256 /dev/nvidia0
b69a5000-b69a6000 rwxs 10b01000 00:0f 8256 /dev/nvidia0
b69a6000-b69a7000 rwxs ecc0a000 00:0f 8256 /dev/nvidia0
b69a7000-b69a8000 rwxs 10b00000 00:0f 8256 /dev/nvidia0
b69a8000-b6daa000 rwxs 10edb000 00:0f 8256 /dev/nvidia0
b6daa000-b71ac000 rwxs 11365000 00:0f 8256 /dev/nvidia0
b7400000-b7421000 rwxp b7400000 00:00 0
b7421000-b7500000 ---p b7421000 00:00 0
b75c2000-b75d3000 rwxs 11255000 00:0f 8256 /dev/nvidia0
b75d3000-b7616000 r-xp 00000000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7616000-b7617000 r-xp 00042000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7617000-b7618000 rwxp 00043000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7618000-b767a000 r-xp 00000000 08:11 5038644 /usr/lib/openmm/libOpenMMCuda.so
b767a000-b767c000 rwxp 00061000 08:11 5038644 /usr/lib/openmm/libOpenMMCuda.so
b767c000-b767e000 rwxp b767c000 00:00 0
b767e000-b76e5000 r-xp 00000000 08:11 5038643 /usr/lib/openmm/libOpenMM.so
b76e5000-b76e7000 rwxp 00066000 08:11 5038643 /usr/lib/openmm/libOpenMM.so
b76e7000-b793d000 rwxp b76e7000 00:00 0
b793d000-b7941000 r-xp 00000000 08:11 4745828 /usr/lib/libXdmcp.so.6.0.0
b7941000-b7942000 rwxp 00003000 08:11 4745828 /usr/lib/libXdmcp.so.6.0.0
b7942000-b7944000 r-xp 00000000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7944000-b7945000 r-xp 00001000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7945000-b7946000 rwxp 00002000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7946000-b795e000 r-xp 00000000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b795e000-b795f000 r-xp 00017000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b795f000-b7960000 rwxp 00018000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b7960000-b7963000 r-xp 00000000 08:11 24035482 /lib/libuuid.so.1.2
b7963000-b7964000 r-xp 00002000 08:11 24035482 /lib/libuuid.so.1.2
b7964000-b7965000 rwxp 00003000 08:11 24035482 /lib/libuuid.so.1.2
b7965000-b797a000 r-xp 00000000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797a000-b797b000 r-xp 00014000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797b000-b797c000 rwxp 00015000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797c000-b797f000 rwxp b797c000 00:00 0
b797f000-b7993000 r-xp 00000000 08:11 24035489 /lib/libz.so.1.2.3.3
b7993000-b7994000 r-xp 00013000 08:11 24035489 /lib/libz.so.1.2.3.3
b7994000-b7995000 rwxp 00014000 08:11 24035489 /lib/libz.so.1.2.3.3
b7995000-b7997000 r-xp 00000000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7997000-b7998000 r-xp 00001000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7998000-b7999000 rwxp 00002000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7999000-b7af5000 r-xp 00000000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af5000-b7af6000 ---p 0015c000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af6000-b7af8000 r-xp 0015c000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af8000-b7af9000 rwxp 0015e000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af9000-b7afc000 rwxp b7af9000 00:00 0
b7afc000-b7b09000 r-xp 00000000 08:11 24035393 /lib/libgcc_s.so.1
b7b09000-b7b0a000 r-xp 0000c000 08:11 24035393 /lib/libgcc_s.so.1
b7b0a000-b7b0b000 rwxp 0000d000 08:11 24035393 /lib/libgcc_s.so.1
b7b0b000-b7b2f000 r-xp 00000000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b2f000-b7b30000 r-xp 00023000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b30000-b7b31000 rwxp 00024000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b31000-b7b32000 rwxp b7b31000 00:00 0
b7b32000-b7c16000 r-xp 00000000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c16000-b7c1a000 r-xp 000e3000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c1a000-b7c1b000 rwxp 000e7000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c1b000-b7c21000 rwxp b7c1b000 00:00 0
b7c21000-b7d0b000 r-xp 00000000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0b000-b7d0c000 ---p 000ea000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0c000-b7d0d000 r-xp 000ea000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0d000-b7d0f000 rwxp 000eb000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0f000-b7d10000 rwxp b7d0f000 00:00 0
b7d10000-b7d25000 r-xp 00000000 08:11 4745778 /usr/lib/libICE.so.6.3.0
b7d25000-b7d26000 rwxp 00014000 08:11 4745778 /usr/lib/libICE.so.6.3.0
b7d26000-b7d28000 rwxp b7d26000 00:00 0
b7d28000-b7d2f000 r-xp 00000000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d2f000-b7d30000 r-xp 00006000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d30000-b7d31000 rwxp 00007000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d31000-b7e0d000 r-xp 00000000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e0d000-b7e13000 r-xp 000dc000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e13000-b7e14000 rwxp 000e2000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e14000-b7e29000 r-xp 00000000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e29000-b7e2a000 r-xp 00014000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e2a000-b7e2b000 rwxp 00015000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e2b000-b7e2e000 rwxp b7e2b000 00:00 0
b7e2e000-b7f63000 r-xp 00000000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f63000-b7f64000 ---p 00135000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f64000-b7f68000 r-xp 00135000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f68000-b7f69000 rwxp 00139000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f69000-b7f6a000 rwxp b7f69000 00:00 0
b7f77000-b7f78000 rwxs ecc08000 00:0f 8256 /dev/nvidia0
b7f78000-b7f79000 rwxs 10ed7000 00:0f 8256 /dev/nvidia0
b7f79000-b7f80000 r-xp 00000000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f80000-b7f81000 r-xp 00006000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f81000-b7f82000 rwxp 00007000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f82000-b7f83000 rwxp b7f82000 00:00 0
b7f83000-b7fea000 r-xp 00000000 08:11 28762387 /home/paco/Desktop/55/continuare/libOpenMM.so
b7fea000-b7fec000 rwxp 00066000 08:11 28762387 /home/paco/Desktop/55/continuare/libOpenMM.so
b7fec000-b7ff0000 rwxp b7fec000 00:00 0
b7ff0000-b7ff1000 r-xp b7ff0000 00:00 0 [vdso]
b7ff1000-b800d000 r-xp 00000000 08:11 24035351 /lib/ld-2.9.so
b800d000-b800e000 r-xp 0001b000 08:11 24035351 /lib/ld-2.9.so
b800e000-b800f000 rwxp 0001c000 08:11 24035351 /lib/ld-2.9.so
bf9f9000-bfa0e000 rwxp bffeb000 00:00 0 [stack]
Aborted
paco@paco:~/Desktop/55/continuare$
---------------------
The temperature of GPU it is 61 degrees Celsius
Questions:
1.Why it stopped after a few ns, with the message:
Error: unspecified launch failure launching kernel kCalculateObcGbsaForces2
2.
- Without libOpenMM.so in working directory (/home/paco/Desktop/55/continuare/)
does not start: mdrun_openmm: error while loading shared libraries: libOpenMM.so:
cannot open shared object file: No such file or directory.
- When put libOpenMM.so directory starts working, but look somewhere:
Successfully loaded plugin /usr/lib/openmm/libOpenMM.so
3. agb parameter file line=<> is being skipped. It is ok?
Thank You
Romica
I could not obtain a trajectory of 100 ns with OpenMM-pr2.
After 7ns my simulation stops with the same message that appears
in OpenMM-pr3 with no running.
Here are portions of md.log:
<
Log file opened on Sat Jun 6 13:59:27 2009
Host: paco pid: 4380 nodeid: 0 nnodes: 1
The Gromacs distribution was built Fri Feb 6 09:33:59 PST 2009 by
cmbruns@cmbruns.stanford.edu (Linux 2.6.18-92.1.22.el5 i686)
G R O M A C S (-:Gyas ROwers Mature At Cryogenic Speed
VERSION 4.0.3_pre (-:Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
mdrun_openmm (-:.
.
.
andersen_seed = 815131
rlist = 100
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 100
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 100
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-05
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
.
.
.
qm_opts:
ngQM = 0
nstvmdout = 0
vmdSocketNumber = 0
blockUntilVmdConnected = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 100 Coulomb: 100 LJ: 100
System total charge: 6.000
Generated table with 50500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 50500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 50500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 557
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest
There are: 1098 Atoms
Successfully loaded plugin /usr/lib/openmm/libOpenMM.so
Successfully loaded plugin /usr/lib/openmm/libOpenMMCuda.so
agb parameter file line=<> is being skipped.
agb parameter file line=<> is being skipped.
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 5.55e-06
Initial temperature: 295.765 K
Started mdrun on node 0 Sat Jun 6 13:59:28 2009
Step Time Lambda
1 0.00200 0.00000
Step Time Lambda
1000 2.00000 0.00000
Step Time Lambda
.
.
.
Step Time Lambda
7665000 15330.00098 0.00000
Step Time Lambda
7666000 15332.00098 0.00000
Step Time Lambda
7667000 15334.00098 0.00000
Step Time Lambda
7668000 15336.00098 0.00000
here stops in md.log
----------------------------
and from terminal after stops:
Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 4.0.5 (single precision)
Note: tpx file_version 58, software version 59
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
directory: /usr/lib/openmm
OpenMM Platform: Cuda
starting mdrun 'Protein'
35000000 steps, 70000.0 ps.
Error: unspecified launch failure launching kernel kCalculateObcGbsaForces2
*** glibc detected *** mdrun_openmm: double free or corruption (fasttop): 0x098409e0 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0xb7a08604]
/lib/tls/i686/cmov/libc.so.6(cfree+0x96)[0xb7a0a5b6]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7beb231]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0xb7bc79fd]
libOpenMM.so[0xb7fcf1ea]
/lib/tls/i686/cmov/libc.so.6(__cxa_finalize+0xc1)[0xb79c7f51]
libOpenMM.so[0xb7f9b804]
libOpenMM.so[0xb7fd986c]
/lib/ld-linux.so.2[0xb7fffa73]
/lib/tls/i686/cmov/libc.so.6(exit+0x89)[0xb79c7bb9]
/usr/lib/openmm/libOpenMMCuda.so[0xb764911d]
/usr/lib/openmm/libOpenMMCuda.so[0xb7626e9e]
libOpenMM.so(_ZN6OpenMM21HarmonicBondForceImpl10calcForcesERNS_17OpenMMContextImplERNS_6StreamE+0x59)[0xb7faa3e9]
libOpenMM.so(_ZN6OpenMM17OpenMMContextImpl10calcForcesEv+0x7d)[0xb7fa17dd]
libOpenMM.so(_ZN6OpenMM18LangevinIntegrator4stepEi+0x43)[0xb7fa62c3]
mdrun_openmm[0x8060f7e]
mdrun_openmm[0x805b50d]
mdrun_openmm[0x8059d6f]
mdrun_openmm[0x805cb46]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe5)[0xb79af775]
mdrun_openmm(__gxx_personality_v0+0x141)[0x804bb71]
======= Memory map: ========
08048000-082a5000 r-xp 00000000 08:11 4743340 /usr/bin/mdrun_openmm
082a5000-082ad000 rwxp 0025d000 08:11 4743340 /usr/bin/mdrun_openmm
082ad000-082b3000 rwxp 082ad000 00:00 0
09777000-09a63000 rwxp 09777000 00:00 0 [heap]
b29ce000-b67a5000 rwxp b29ce000 00:00 0
b67a5000-b68a5000 rwxs 10408000 00:0f 8256 /dev/nvidia0
b68a5000-b69a5000 rwxs 10b03000 00:0f 8256 /dev/nvidia0
b69a5000-b69a6000 rwxs 10b01000 00:0f 8256 /dev/nvidia0
b69a6000-b69a7000 rwxs ecc0a000 00:0f 8256 /dev/nvidia0
b69a7000-b69a8000 rwxs 10b00000 00:0f 8256 /dev/nvidia0
b69a8000-b6daa000 rwxs 10edb000 00:0f 8256 /dev/nvidia0
b6daa000-b71ac000 rwxs 11365000 00:0f 8256 /dev/nvidia0
b7400000-b7421000 rwxp b7400000 00:00 0
b7421000-b7500000 ---p b7421000 00:00 0
b75c2000-b75d3000 rwxs 11255000 00:0f 8256 /dev/nvidia0
b75d3000-b7616000 r-xp 00000000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7616000-b7617000 r-xp 00042000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7617000-b7618000 rwxp 00043000 08:11 5351497 /usr/local/cuda/lib/libcudart.so.2.2
b7618000-b767a000 r-xp 00000000 08:11 5038644 /usr/lib/openmm/libOpenMMCuda.so
b767a000-b767c000 rwxp 00061000 08:11 5038644 /usr/lib/openmm/libOpenMMCuda.so
b767c000-b767e000 rwxp b767c000 00:00 0
b767e000-b76e5000 r-xp 00000000 08:11 5038643 /usr/lib/openmm/libOpenMM.so
b76e5000-b76e7000 rwxp 00066000 08:11 5038643 /usr/lib/openmm/libOpenMM.so
b76e7000-b793d000 rwxp b76e7000 00:00 0
b793d000-b7941000 r-xp 00000000 08:11 4745828 /usr/lib/libXdmcp.so.6.0.0
b7941000-b7942000 rwxp 00003000 08:11 4745828 /usr/lib/libXdmcp.so.6.0.0
b7942000-b7944000 r-xp 00000000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7944000-b7945000 r-xp 00001000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7945000-b7946000 rwxp 00002000 08:11 4745817 /usr/lib/libXau.so.6.0.0
b7946000-b795e000 r-xp 00000000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b795e000-b795f000 r-xp 00017000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b795f000-b7960000 rwxp 00018000 08:11 4746785 /usr/lib/libxcb.so.1.1.0
b7960000-b7963000 r-xp 00000000 08:11 24035482 /lib/libuuid.so.1.2
b7963000-b7964000 r-xp 00002000 08:11 24035482 /lib/libuuid.so.1.2
b7964000-b7965000 rwxp 00003000 08:11 24035482 /lib/libuuid.so.1.2
b7965000-b797a000 r-xp 00000000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797a000-b797b000 r-xp 00014000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797b000-b797c000 rwxp 00015000 08:11 24053091 /lib/tls/i686/cmov/libpthread-2.9.so
b797c000-b797f000 rwxp b797c000 00:00 0
b797f000-b7993000 r-xp 00000000 08:11 24035489 /lib/libz.so.1.2.3.3
b7993000-b7994000 r-xp 00013000 08:11 24035489 /lib/libz.so.1.2.3.3
b7994000-b7995000 rwxp 00014000 08:11 24035489 /lib/libz.so.1.2.3.3
b7995000-b7997000 r-xp 00000000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7997000-b7998000 r-xp 00001000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7998000-b7999000 rwxp 00002000 08:11 24053071 /lib/tls/i686/cmov/libdl-2.9.so
b7999000-b7af5000 r-xp 00000000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af5000-b7af6000 ---p 0015c000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af6000-b7af8000 r-xp 0015c000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af8000-b7af9000 rwxp 0015e000 08:11 24053065 /lib/tls/i686/cmov/libc-2.9.so
b7af9000-b7afc000 rwxp b7af9000 00:00 0
b7afc000-b7b09000 r-xp 00000000 08:11 24035393 /lib/libgcc_s.so.1
b7b09000-b7b0a000 r-xp 0000c000 08:11 24035393 /lib/libgcc_s.so.1
b7b0a000-b7b0b000 rwxp 0000d000 08:11 24035393 /lib/libgcc_s.so.1
b7b0b000-b7b2f000 r-xp 00000000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b2f000-b7b30000 r-xp 00023000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b30000-b7b31000 rwxp 00024000 08:11 24053073 /lib/tls/i686/cmov/libm-2.9.so
b7b31000-b7b32000 rwxp b7b31000 00:00 0
b7b32000-b7c16000 r-xp 00000000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c16000-b7c1a000 r-xp 000e3000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c1a000-b7c1b000 rwxp 000e7000 08:11 4746702 /usr/lib/libstdc++.so.6.0.10
b7c1b000-b7c21000 rwxp b7c1b000 00:00 0
b7c21000-b7d0b000 r-xp 00000000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0b000-b7d0c000 ---p 000ea000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0c000-b7d0d000 r-xp 000ea000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0d000-b7d0f000 rwxp 000eb000 08:11 4745811 /usr/lib/libX11.so.6.2.0
b7d0f000-b7d10000 rwxp b7d0f000 00:00 0
b7d10000-b7d25000 r-xp 00000000 08:11 4745778 /usr/lib/libICE.so.6.3.0
b7d25000-b7d26000 rwxp 00014000 08:11 4745778 /usr/lib/libICE.so.6.3.0
b7d26000-b7d28000 rwxp b7d26000 00:00 0
b7d28000-b7d2f000 r-xp 00000000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d2f000-b7d30000 r-xp 00006000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d30000-b7d31000 rwxp 00007000 08:11 4745809 /usr/lib/libSM.so.6.0.0
b7d31000-b7e0d000 r-xp 00000000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e0d000-b7e13000 r-xp 000dc000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e13000-b7e14000 rwxp 000e2000 08:11 4744832 /usr/lib/libfftw3f.so.3.1.2
b7e14000-b7e29000 r-xp 00000000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e29000-b7e2a000 r-xp 00014000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e2a000-b7e2b000 rwxp 00015000 08:11 24053076 /lib/tls/i686/cmov/libnsl-2.9.so
b7e2b000-b7e2e000 rwxp b7e2b000 00:00 0
b7e2e000-b7f63000 r-xp 00000000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f63000-b7f64000 ---p 00135000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f64000-b7f68000 r-xp 00135000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f68000-b7f69000 rwxp 00139000 08:11 4746791 /usr/lib/libxml2.so.2.6.32
b7f69000-b7f6a000 rwxp b7f69000 00:00 0
b7f77000-b7f78000 rwxs ecc08000 00:0f 8256 /dev/nvidia0
b7f78000-b7f79000 rwxs 10ed7000 00:0f 8256 /dev/nvidia0
b7f79000-b7f80000 r-xp 00000000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f80000-b7f81000 r-xp 00006000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f81000-b7f82000 rwxp 00007000 08:11 24053095 /lib/tls/i686/cmov/librt-2.9.so
b7f82000-b7f83000 rwxp b7f82000 00:00 0
b7f83000-b7fea000 r-xp 00000000 08:11 28762387 /home/paco/Desktop/55/continuare/libOpenMM.so
b7fea000-b7fec000 rwxp 00066000 08:11 28762387 /home/paco/Desktop/55/continuare/libOpenMM.so
b7fec000-b7ff0000 rwxp b7fec000 00:00 0
b7ff0000-b7ff1000 r-xp b7ff0000 00:00 0 [vdso]
b7ff1000-b800d000 r-xp 00000000 08:11 24035351 /lib/ld-2.9.so
b800d000-b800e000 r-xp 0001b000 08:11 24035351 /lib/ld-2.9.so
b800e000-b800f000 rwxp 0001c000 08:11 24035351 /lib/ld-2.9.so
bf9f9000-bfa0e000 rwxp bffeb000 00:00 0 [stack]
Aborted
paco@paco:~/Desktop/55/continuare$
---------------------
The temperature of GPU it is 61 degrees Celsius
Questions:
1.Why it stopped after a few ns, with the message:
Error: unspecified launch failure launching kernel kCalculateObcGbsaForces2
2.
- Without libOpenMM.so in working directory (/home/paco/Desktop/55/continuare/)
does not start: mdrun_openmm: error while loading shared libraries: libOpenMM.so:
cannot open shared object file: No such file or directory.
- When put libOpenMM.so directory starts working, but look somewhere:
Successfully loaded plugin /usr/lib/openmm/libOpenMM.so
3. agb parameter file line=<> is being skipped. It is ok?
Thank You
Romica
-
Mark Friedrichs
- Posts: 32
- Joined: Fri Jun 09, 2006 11:23 am
RE: Error: too many resources requested for launc
Not sure why it is crashing. The problem w/ libOpenMM.so that you mention suggests that you don't have /usr/lib/openmm (or wherever the libs are located) set in your env variable LD_LIBRARY_PATH. If the program is loading libs that are inconsistent w/ one another that could lead to crashes. Perhaps you can get rid of all the OpenMM-related libs and start over w/ just one set of libs on your machine.
The line 'agb parameter file line=<> is being skipped.' can be ignored.
The line 'agb parameter file line=<> is being skipped.' can be ignored.