date:20180106

Re: [gmx-users] GROMACS-GPU enabled installation error

2018-01-06 Thread David van der Spoel


Den 2018-01-06 kl. 22:20, skrev Joydeep Munshi:

Hello,

I am trying to install Gromacs 5.1.5 with GPU enabled version. I have
Nvidia Geforce GTX1080 GPU card in my system and Cuda 9.1.85 installed as
my nvcc. While running cmake command as mentioned below, I am succssfully
able to generate the makefiles in build directory. However, while running
make after that, I am facing with an error. Could you please help me out
with resolving the issue?


You need to throw away your CMakeCache.txt file since it has leftovers 
from a previous build. Alternatively, you may have two conflicting CUDA 
installations.


In addition you should consider installing the latest version instead 
(2016.4 for stable or 2018.beta for the upcoming release).




*cmake *comamnd used before running *make*:

*cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_GPU=on-DGMX_BUILD_MDRUN_ONLY=on
-DGMX_BINARY_SUFFIX=_cuda  -DGMX_LIBS_SUFFIX=_cuda
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.1*


*make *error:

  */bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
* /usr/bin/install -c -m 644 fftw3f.pc
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
*Making install in threads*
*Making install in tests*
*Making install in mpi*
*Making install in doc*
*Making install in FAQ*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
* /usr/bin/install -c -m 644
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info

/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-1
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-2
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
* install-info
--info-dir='/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info/fftw3.info
'*
*Making install in tools*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
*  /bin/bash ../libtool   --mode=install /usr/bin/install -c fftwf-wisdom
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
*libtool: install: /usr/bin/install -c fftwf-wisdom
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin/fftwf-wisdom*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
* /usr/bin/install -c fftw-wisdom-to-conf
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
* /usr/bin/install -c -m 644
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/tools/fftw-wisdom-to-conf.1
fftwf-wisdom.1
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
*Making install in m4*
*[  0%] Completed 'fftwBuild'*
*[  0%] Built target fftwBuild*
*[  0%] Generating baseversion-gen.c*
*[  1%] Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o*
*nvcc fatal   : Unsupported gpu architecture 'compute_20'*
*CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:207 (message):*
*  Error generating*
*
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o*


*src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o'
failed*
*make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o]
Error 1*
*CMakeFiles/Makefile2:1291: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed*
*make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2*
*Makefile:160: recipe for target 'all' failed*
*make: *** [all] Error 2*

*Thanks and regards,*
*Joydeep Munshi,*
*Graduate Research Assistant,*
*Packard Lab 375,*
*Mechanical Engineering and Mechanics,*
*Lehigh University*
*Contact: (484)-821-6702*




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read

[gmx-users] GROMACS-GPU enabled installation error

2018-01-06 Thread Joydeep Munshi

Hello,

I am trying to install Gromacs 5.1.5 with GPU enabled version. I have
Nvidia Geforce GTX1080 GPU card in my system and Cuda 9.1.85 installed as
my nvcc. While running cmake command as mentioned below, I am succssfully
able to generate the makefiles in build directory. However, while running
make after that, I am facing with an error. Could you please help me out
with resolving the issue?

*cmake *comamnd used before running *make*:

*cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_GPU=on-DGMX_BUILD_MDRUN_ONLY=on
-DGMX_BINARY_SUFFIX=_cuda  -DGMX_LIBS_SUFFIX=_cuda
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.1*


*make *error:

 */bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
* /usr/bin/install -c -m 644 fftw3f.pc
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
*Making install in threads*
*Making install in tests*
*Making install in mpi*
*Making install in doc*
*Making install in FAQ*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
* /usr/bin/install -c -m 644
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info

/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-1
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-2
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
* install-info
--info-dir='/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info/fftw3.info
'*
*Making install in tools*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
*  /bin/bash ../libtool   --mode=install /usr/bin/install -c fftwf-wisdom
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
*libtool: install: /usr/bin/install -c fftwf-wisdom
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin/fftwf-wisdom*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
* /usr/bin/install -c fftw-wisdom-to-conf
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
* /bin/mkdir -p
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
* /usr/bin/install -c -m 644
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/tools/fftw-wisdom-to-conf.1
fftwf-wisdom.1
'/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
*Making install in m4*
*[  0%] Completed 'fftwBuild'*
*[  0%] Built target fftwBuild*
*[  0%] Generating baseversion-gen.c*
*[  1%] Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o*
*nvcc fatal   : Unsupported gpu architecture 'compute_20'*
*CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:207 (message):*
*  Error generating*
*
/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o*


*src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o'
failed*
*make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o]
Error 1*
*CMakeFiles/Makefile2:1291: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed*
*make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2*
*Makefile:160: recipe for target 'all' failed*
*make: *** [all] Error 2*

*Thanks and regards,*
*Joydeep Munshi,*
*Graduate Research Assistant,*
*Packard Lab 375,*
*Mechanical Engineering and Mechanics,*
*Lehigh University*
*Contact: (484)-821-6702*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] energy minimization

2018-01-06 Thread rose rahmani

Hi,

I want to calculate the number of density profile of water.the initial .gro
file which i have,has amino acid in itself, which should not be present in
this analyze. So, i had to remove amino acid, and then, when i wanted to do
energy minimization again, it's crushed and gave me step files.
maybe it's because of modifying the initial gro file but i didn't have any
choice i think so! because i have another structures in initial.gro file
which i don't want to modify their coordinates.and all structure are in the
center of box and the rest of the box should be empty.
would you please help me? what is the alternative?

with regards




this is em.job

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps= 5000
Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
815
Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
4307
Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
4307
Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
4302
Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
4303
Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
4303
Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
4303
Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
4303
Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
4303
Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
4303
Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
4302
Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
4302
Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
4301
Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
4303

step 14: Water molecule starting at atom 2018 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 14: Water molecule starting at atom 1265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
2018^M
step 15: Water molecule starting at atom 1331 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
atom= 4301
Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
4303
Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
4301
Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
4301
Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
4301
Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
4301

   140,1
.
.
.
.
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Re: [gmx-users] GROMACS-GPU enabled installation error

[gmx-users] GROMACS-GPU enabled installation error

[gmx-users] energy minimization

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