[sushil@gwacsg01 lam-0.00000]$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2015 NVIDIA Corporation
Built on Tue_Aug_11_14:27:32_CDT_2015
Cuda compilation tools, release 7.5, V7.5.17
[sushil@gwacsg01 lam-0.00000]$ /home/sushil/sire.app/bin/somd-freenrg -C ../../00.core/sim.cfg -t ../../00.core/ligand.parm7 -c ../../00.core/ligand.rst7 -p CUDA -d 0 -l 0.00000
Starting /home/sushil/sire.app/bin/somd-freenrg: number of threads equals 24
==============================================================
Sending anonymous Sire usage statistics to http://siremol.org.
For more information, see http://siremol.org/analytics
To disable, set the environment variable 'SIRE_DONT_PHONEHOME' to 1
To see the information sent, set the environment variable
SIRE_VERBOSE_PHONEHOME equal to 1. To silence this message, set
the environment variable SIRE_SILENT_PHONEHOME to 1.
==============================================================
Loading configuration information from file ../../00.core/sim.cfg
Running a somd-freenrg calculation using files ../../00.core/ligand.parm7, ../../00.core/ligand.rst7 and ../../00.core/MORPH.charge.pert.
Using parameters:
===============
andersen == True
barostat == True
buffered coordinates frequency == 100
center solute == True
constraint == allbonds
crdfile == ../../00.core/ligand.rst7
cutoff distance == 9 angstrom
cutoff type == cutoffperiodic
energy frequency == 100
equilibrate == True
equilibration iterations == 50
gpu == 0
lambda_val == 0.0
minimize == True
morphfile == ../../00.core/MORPH.charge.pert
ncycles == 50
nmoves == 1000
platform == CUDA
precision == mixed
save coordinates == True
topfile == ../../00.core/ligand.parm7
===============
### Running Single Topology Molecular Dynamics Free Energy on gwacsg29 ###
###================Setting up calculation=====================###
Re-initialisation of OpenMMFrEnergyST from datastream
Index GPU = 0
Loaded a restart file on which we have performed 0 moves.
There are 3727 atoms in the group
###===========================================================###
###======================Equilibration========================###
Running lambda equilibration to lambda=0.0.
Traceback (most recent call last):
File "/bwfefs/home/sushil/sire.app/pkgs/sire-2017.1.0/share/Sire/scripts/somd-freenrg.py", line 146, in <module>
OpenMMMD.runFreeNrg(params)
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner
retval = func()
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/OpenMMMD.py", line 1634, in runFreeNrg
system = integrator.annealSystemToLambda(system, equil_timestep.val, equil_iterations.val)
RuntimeError: Error launching CUDA compiler: 32512
sh: /usr/local/cuda/bin/nvcc: No such file or directory
[sushil@gwacsg29 lam-0.00000]$ which nvcc
/gwfefs/opt/x86_64/cuda/7.5/bin/nvcc
I wonder if the path for nvcc is added by sire and if I can assign it somehow?
Thanking you,
Sushil
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export CUDA_HOME=/usr/local/cuda-7.5
export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:$LD_LIBRARY_PATH
export PATH=${CUDA_HOME}/bin:${PATH}
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[sushil@gwacsg15 lam-0.00000]$ echo $CUDA_HOME
/gwfefs/opt/x86_64/cuda/7.5
[sushil@gwacsg15 lam-0.00000]$ echo $LD_LIBRARY_PATH
/gwfefs/opt/x86_64/cuda/7.5/lib64:/gwfefs/opt/x86_64/cuda/7.5/lib64:/gwfefs/opt/x86_64/cuda/7.5/lib:/gwfefs/home/sushil/soft/mysoft/amber-acs/amber16/lib:/bwfefs/opt/x86_64/intel/impi/2017.3.196/intel64/lib:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/compiler/lib/intel64:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/compiler/lib/intel64_lin:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/mpi/intel64/lib:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/mpi/mic/lib:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/ipp/lib/intel64:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/compiler/lib/intel64:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/mkl/lib/intel64:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/tbb/lib/intel64/gcc4.4:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/debugger_2017/iga/lib:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/debugger_2017/libipt/intel64/lib:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/daal/lib/intel64_lin:/bwfefs/opt/x86_64/intel/parallel_studio_xe_2017/compilers_and_libraries_2017//linux/daal/../tbb/lib/intel64_lin/gcc4.4:/gwfefs/home/sushil/soft/mysoft/boost-1.63/build/lib
[sushil@gwacsg15 lam-0.00000]$ which nvcc
/gwfefs/opt/x86_64/cuda/7.5/bin/nvcc
[sushil@gwacsg15 lam-0.00000]$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2015 NVIDIA Corporation
Built on Tue_Aug_11_14:27:32_CDT_2015
Cuda compilation tools, release 7.5, V7.5.17
[sushil@gwacsg15 lam-0.00000]$ /home/sushil/sire.app/bin/somd-freenrg -C ../../00.core/sim.cfg -t ../../00.core/ligand.parm7 -c ../../00.core/ligand.rst7 -p CUDA -d 0 -l 0.1
lambda_val == 0.1
minimize == True
morphfile == ../../00.core/MORPH.charge.pert
ncycles == 50
nmoves == 1000
platform == CUDA
precision == mixed
save coordinates == True
topfile == ../../00.core/ligand.parm7
===============
### Running Single Topology Molecular Dynamics Free Energy on gwacsg15 ###
###================Setting up calculation=====================###
New run. Loading input and creating restart
lambda is 0.1
Create the System...
Selecting dummy groups
Creating force fields...
Setting up the simulation with random seed 550296
Setting up moves...
Created a MD move that uses OpenMM for all molecules on 0
Generated random seed number 550296
Saving restart
Setting up sim file.
There are 3727 atoms in the group
###===========================================================###
###======================Equilibration========================###
Running lambda equilibration to lambda=0.1.
Traceback (most recent call last):
File "/bwfefs/home/sushil/sire.app/pkgs/sire-2017.1.0/share/Sire/scripts/somd-freenrg.py", line 146, in <module>
OpenMMMD.runFreeNrg(params)
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner
retval = func()
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/OpenMMMD.py", line 1634, in runFreeNrg
system = integrator.annealSystemToLambda(system, equil_timestep.val, equil_iterations.val)
RuntimeError: Error launching CUDA compiler: 32512
sh: /usr/local/cuda/bin/nvcc: No such file or directory
Do you think this is not related to Sire and it calls "nvcc" or $CUDA_PATH/bin/nvcc? Also, if I set -d to 1,2 or 3 (each node had 4 gpu cards), I get another error.
[sushil@gwacsg15 lam-0.00000]$ nvidia-smi
Sat Dec 16 07:53:17 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 367.48 Driver Version: 367.48 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 Tesla K20Xm Off | 0000:04:00.0 Off | 0 |
| N/A 48C P0 141W / 235W | 277MiB / 5699MiB | 98% Default |
+-------------------------------+----------------------+----------------------+
| 1 Tesla K20Xm Off | 0000:09:00.0 Off | 0 |
| N/A 32C P8 30W / 235W | 0MiB / 5699MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 2 Tesla K20Xm Off | 0000:85:00.0 Off | 0 |
| N/A 34C P8 19W / 235W | 0MiB / 5699MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 Tesla K20Xm Off | 0000:88:00.0 Off | 0 |
| N/A 49C P0 143W / 235W | 183MiB / 5699MiB | 98% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 19056 C pmemd.cuda 275MiB |
| 3 12438 C pmemd.cuda 181MiB |
+-----------------------------------------------------------------------------+
[sushil@gwacsg15 lam-0.00000]$ /home/sushil/sire.app/bin/somd-freenrg -C ../../00.core/sim.cfg -t ../../00.core/ligand.parm7 -c ../../00.core/ligand.rst7 -p CUDA -d 1 -l 0.1
Starting /home/sushil/sire.app/bin/somd-freenrg: number of threads equals 24
Loading configuration information from file ../../00.core/sim.cfg
Running a somd-freenrg calculation using files ../../00.core/ligand.parm7, ../../00.core/ligand.rst7 and ../../00.core/MORPH.charge.pert.
Using parameters:
===============
andersen == True
barostat == True
buffered coordinates frequency == 100
center solute == True
constraint == allbonds
crdfile == ../../00.core/ligand.rst7
cutoff distance == 9 angstrom
cutoff type == cutoffperiodic
energy frequency == 100
equilibrate == True
equilibration iterations == 50
gpu == 1
lambda_val == 0.1
minimize == True
morphfile == ../../00.core/MORPH.charge.pert
ncycles == 50
nmoves == 1000
platform == CUDA
precision == mixed
save coordinates == True
topfile == ../../00.core/ligand.parm7
===============
### Running Single Topology Molecular Dynamics Free Energy on gwacsg15 ###
###================Setting up calculation=====================###
New run. Loading input and creating restart
lambda is 0.1
Create the System...
Selecting dummy groups
Creating force fields...
Setting up the simulation with random seed 195923
Setting up moves...
Created a MD move that uses OpenMM for all molecules on 1
Generated random seed number 195923
Saving restart
Setting up sim file.
There are 3727 atoms in the group
###===========================================================###
###======================Equilibration========================###
Running lambda equilibration to lambda=0.1.
Traceback (most recent call last):
File "/bwfefs/home/sushil/sire.app/pkgs/sire-2017.1.0/share/Sire/scripts/somd-freenrg.py", line 146, in <module>
OpenMMMD.runFreeNrg(params)
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner
retval = func()
File "/home/sushil/sire.app/lib/python3.5/site-packages/Sire/Tools/OpenMMMD.py", line 1634, in runFreeNrg
system = integrator.annealSystemToLambda(system, equil_timestep.val, equil_iterations.val)
RuntimeError: Illegal value for CudaDeviceIndex: 1
Regards,
Sushil
Dr Antonia Mey
University of Edinburgh
School of Chemistry
Joseph Black Building
Edinburgh
EH9 3FJ
Tel: +44 1316507748
Email: anton...@gmail.com
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Mon Dec 18 21:07:04 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 367.48 Driver Version: 367.48 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 Tesla K20Xm Off | 0000:04:00.0 Off | 0 |
| N/A 41C P0 137W / 235W | 183MiB / 5699MiB | 99% Default |
+-------------------------------+----------------------+----------------------+
| 1 Tesla K20Xm Off | 0000:09:00.0 Off | 0 |
| N/A 34C P0 74W / 235W | 214MiB / 5699MiB | 24% Default |
+-------------------------------+----------------------+----------------------+
| 2 Tesla K20Xm Off | 0000:85:00.0 Off | 0 |
| N/A 35C P0 69W / 235W | 215MiB / 5699MiB | 22% Default |
+-------------------------------+----------------------+----------------------+
| 3 Tesla K20Xm Off | 0000:88:00.0 Off | 0 |
| N/A 29C P8 31W / 235W | 0MiB / 5699MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 31080 C pmemd.cuda 181MiB |
| 1 20885 C ./namd2 212MiB |
| 2 20885 C ./namd2 213MiB |
+-----------------------------------------------------------------------------+
[sushil@gwacsg09 test-gpu]$
Antonia
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Dr Antonia Mey
University of Edinburgh
School of Chemistry
Joseph Black Building
Edinburgh
EH9 3FJ
Tel: +44 1316507748
Email: anton...@gmail.com
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--Dr Antonia MeyUniversity of EdinburghSchool of ChemistryJoseph Black BuildingEdinburghEH9 3FJTel: +44 1316507748Email: anton...@gmail.com
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Dr Antonia Mey
University of Edinburgh
School of Chemistry
Joseph Black Building
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EH9 3FJ
Tel: +44 1316507748
Email: anton...@gmail.com
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--Dr Antonia MeyUniversity of EdinburghSchool of ChemistryJoseph Black BuildingEdinburghEH9 3FJTel: +44 1316507748Email: anton...@gmail.com
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Dr Antonia Mey
University of Edinburgh
School of Chemistry
Joseph Black Building
Edinburgh
EH9 3FJ
Tel: +44 1316507748
Email: anton...@gmail.com
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<PMF-Kelm2-to-4c.png>