Hi!
tried with cmake 2.8.0 and it seems that is working!!!!
Thanks for all Szilárd :)
Jordi Inglés
El 29/03/11 13:00, Szilárd Páll escribió:
Hi,
I've diff-ed the cache file you sent me against the one I generated
and I couldn't see anything relevant. Neither does the verbose CMake
output suggest anything useful, but that it tries to copy the
mdrun-gpu binary from a location where it obviously does not exist. I
don't even have this "CMakeRelink.dir" directory in my build tree.
I googled around a found the same issue being mentioned in a few
places, but couldn't figure out what the reason/solution is.
A few more things you could try if you haven't tried yet:
1) 4.5.4 (does it produce the same error?);
2) Run cmake in a _clean_ build directory;
3) Try a different (possibly earlier) CMake version, for me it works
fine with 2.8.0 and actually the latest version I used was AFAIR
2.8.2.
Cheers,
--
Szilárd
On Tue, Mar 29, 2011 at 8:52 AM, Jordi Inglés<jordi.ing...@qi.ub.es> wrote:
Thanks Szilárd for your fast mail,
but it seems that is still failing and don't appears any new error. With
BUILD_SHARED_LIBS flag it seems that it pass the library error but I receive
a similar error with the executable (see attached file) mdrun-gpu, but this
executable exist in other directory:
-rwxr-xr-x 1 root root 3433307 Mar 29 08:31 mdrun-gpu
I attach also the CMakeCache list if it can help.
Thanks for any advise!
jordi inglés
El 28/03/11 21:50, Szilárd Páll escribió:
Hi Jordi,
I've never seen this error or anything similar, but I can give you hints.
The CMake build system first generates binaries in the build directory
which are also runnable from there (are linked against libs located in
the build three). When you do a "make install[-mdrun]", howerver,
these binaries get relinked to rewrite the library dependencies. lt
seems that in your case this last step fails.
What you can do is to try to run
$ make install-mdrun VERBOSE=1 ,
maybe you can see something on the verbose output. For reference I've
attached a verbose output of the above command I just generated.
Otherwise, you could set BUILD_SHARED_LIBS=OFF, case in which internal
Gromacs libraries will be linked statically.
Cheers,
--
Szilárd
2011/3/28 Jordi Inglés<jordi.ing...@qi.ub.es>:
Hi,
I'm compiling gromacs with gcc compiler (v 4.3.2), cmake (2.8.3) and
OpenMM
2.0 in a SLES 11.0 Linux.
I follow the instructions in the page and it seems that the compilation
goes
fine.
gpu01:/scratch/jingles/gcc/gromacs-4.5.3 # ls -ltra src/kernel/mdrun-gpu
-rwxr-xr-x 1 root root 518294 Mar 28 10:16 src/kernel/mdrun-gpu
But when I try to install the application I obtain this error:
make install-mdrun
-- Using default binary suffix: "-gpu"
-- Using default library suffix: "_gpu"
-- Using internal FFT library - fftpack
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/jingles/gcc/gromacs-4.5.3
Linking CXX static library libgmx_gpu_utils.a
[ 0%] Built target gmx_gpu_utils
[ 78%] Built target gmx
[ 92%] Built target md
[ 98%] Built target gmxpreprocess
[ 98%] Built target openmm_api_wrapper
Linking CXX executable mdrun-gpu
[100%] Built target mdrun
Scanning dependencies of target install-mdrun
[100%] Installing mdrun
-- Install configuration: "Release"
-- Install component: "libraries"
CMake Error at
/scratch/jingles/gcc/gromacs-4.5.3/src/gmxlib/cmake_install.cmake:38
(FILE):
file INSTALL cannot find
"/scratch/jingles/gcc/gromacs-4.5.3/src/gmxlib/CMakeFiles/CMakeRelink.dir/libgmx_gpu.so.6".
Call Stack (most recent call first):
/scratch/jingles/gcc/gromacs-4.5.3/src/cmake_install.cmake:37 (INCLUDE)
/scratch/jingles/gcc/gromacs-4.5.3/cmake_install.cmake:40 (INCLUDE)
make[3]: *** [src/kernel/CMakeFiles/install-mdrun] Error 1
make[2]: *** [src/kernel/CMakeFiles/install-mdrun.dir/all] Error 2
make[1]: *** [src/kernel/CMakeFiles/install-mdrun.dir/rule] Error 2
make: *** [install-mdrun] Error 2
It seems that CMakeRelink.dir it's empty (I supose that the own
compilation
cleans it). the libgmx_gpu.so.6 exist in her source directory:
gpu01:/scratch/jingles/gcc/gromacs-4.5.3 # ls -ltra
src/gmxlib/libgmx_gpu.so*
-rwxr-xr-x 1 root root 3378435 Mar 28 10:11 src/gmxlib/libgmx_gpu.so.6
lrwxrwxrwx 1 root root 15 Mar 28 10:11 src/gmxlib/libgmx_gpu.so ->
libgmx_gpu.so.6
Have you got any idea about the problem? I tried to compile with the
--debut-output --debug-trycompile options of cmake that don't clean the
compilation after finishing for checking that CMakeRelink.dir is empty or
not, but it seems that still continues empty.
Thanks for any advise.
Jordi Inglés Camats
--
__________________________________
Jordi Inglés Camats
Institut de Química Teòrica Computacional (IQTCUB)
Facultat de Física i Química
Despatx 766
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__________________________________
Jordi Inglés Camats
Institut de Química Teòrica Computacional (IQTCUB)
Facultat de Física i Química
Despatx 766
--
__________________________________
Jordi Inglés Camats
Institut de Química Teòrica Computacional (IQTCUB)
Facultat de Física i Química
Despatx 766
--
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