Re: [gmx-users] OpenSuse 12.1 + CUDA Installation Error
On 25.07.2013 04:25, Carlos Bueno wrote: I added all the repositories and installed all you told me. And that solved the problem for one of the computers The others still have an error in make: [ 55%] Building NVCC (Device) object src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o /home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(216): error: identifier nbnxn_alloc_t is undefined /home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(217): error: identifier nbnxn_free_t is undefined 2 errors detected in the compilation of /tmp/tmpxft_76ad_-11_nbnxn_cuda.compute_20.cpp2.i. CMake Error at CMakeFiles/nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:256 (message): Can you look in the first part of your cmake log to find out which gcc version has been used? What does `g++ -v` say? M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OpenSuse 12.1 + CUDA Installation Error
On 24.07.2013 04:08, Carlos Bueno wrote:
*Hi,*
*I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
*I have installed cuda 5.0 and the nvidia cards. **I have tried with
different parameters for cmake:*
How did you install Cuda5? What did you install and how?
I have one OpenSuSE 12.1 box that works as a cluster head
and serves to gpu-clusters. Every software except the
nvidia gpu driver is installed on this box for usage by
the nodes.
Installing a gpu-ready OpenSuSE 12.1 involves (for example, YMMD)
* add community- and extra-repositories through yast/repositories,
these involve (here):
(a) included in yast/repositories (activate only)
Packman Repository
openSUSE BuildService - devel:languages:perl
openSUSE BuildService - devel:languages:python
Education
science
(b) extra (add manually or ba script)
devel:/tools
devel:/libraries:/c_c++
devel:/gcc
you can do the latter by script:
#
#!/bin/sh
Uri[1]=http://download.opensuse.org/repositories/devel:/tools/openSUSE_12.1/;
Name[1]=devel:/tools
Uri[2]=http://download.opensuse.org/repositories/devel:/libraries:/c_c++/openSUSE_12.1/;
Name[2]=devel:/libraries:/c_c++
Uri[3]=http://download.opensuse.org/repositories/devel:/gcc/openSUSE_12.1/;
Name[3]=devel:/gcc
#
for i in 1 2 3; do
zypper --gpg-auto-import-keys ar ${Uri[i]} ${Name[i]}
zypper modifyrepo --refresh ${Name[i]}
done
#
* install gcc 4.6 / g++ 4.6 through yast
* install fftw 3.3.3 through yast, look for the following packages:
gpuclu:~ # rpm -qa |grep fftw
libfftw3-3-3.3.3-5.1.x86_64
fftw3-devel-3.3.3-5.1.x86_64
fftw3-3.3-18.1.3.x86_64
fftw3-threads-3.3-18.1.3.x86_64
fftw3-threads-devel-3.3.3-5.1.x86_64
libfftw3_threads3-3.3.3-5.1.x86_64
* install blas-devel, lapack-devel, gsl-devel through yast
* Important: remove everything Nvidia-related stuff through yast, reboot
* download and install (compile) the gpu driver
NVIDIA-Linux-x86_64-319.32.run
check if it functions properly (after reboot)
* download and install CUDA from Nvidia:
cuda_5.0.35_linux_64_suse12.1-1.run
if everything works, the command
nvidia-smi
should display some meaningful output.
my € 0.05
M.
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[gmx-users] OpenSuse 12.1 + CUDA Installation Error
*Hi,* *I keep getting errors when I try to install gromacs in OpenSuse 12.1.* *I have installed cuda 5.0 and the nvidia cards. **I have tried with different parameters for cmake:* cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *When I make, this error appears:* make [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_avx_256_single.c.o make[2]: *** No hay ninguna regla para construir el objetivo `//home/cuda/Programas/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', necesario para `src/gmxlib/libgmx.so.8'. Alto. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 *So I decided to compile the fftw library myself with the command:* ./configure --enable-single --enable-shared --enable-sse2 --enable-avx * * *and I think that worked but then this error appears:* cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda make [ 64%] Building NVCC (Device) object src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o /home/cuda3/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(216): error: identifier nbnxn_alloc_t is undefined /home/cuda3/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(217): error: identifier nbnxn_free_t is undefined 2 errors detected in the compilation of /tmp/tmpxft_76f4_-11_nbnxn_cuda.compute_20.cpp2.i. CMake Error at CMakeFiles/nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:256 (message): Error generating file /home/cuda3/Programas/gromacs-4.6.3/build/src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o make[2]: *** [src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o] Error 1 make[1]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2 make: *** [all] Error 2 *I need to install with cuda, nevertheless I tried without to see if that would work:* cmake .. make Linking CXX shared library libgmx.so [ 65%] Built target gmx make: *** [all] Error 2 *And to see if I had not installed the library correctly I tried* cmake .. -DGMX_BUILD_OWN_FFTW=ON make [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_avx_256_single.c.o make[2]: *** No hay ninguna regla para construir el objetivo `//home/cuda/Programas/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', necesario para `src/gmxlib/libgmx.so.8'. Alto. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 *I think the problem is related to the PC's (I have three clones) because I have installed Gromacs+CUDA in Ubuntu 12.04 without problems.* *Any suggestions would be very appreciated.* *Thanks* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
