On Mon, Nov 30, 2015 at 11:20 PM, Mijiddorj Batsaikhan <
b.mijiddorj.gmail.com> wrote:
> Here I attached my last log file.
>
> my cofiguration line and last several lines are here:
>
> *./configure -cuda_DPFP gnu*
>
> ######
> If you have not already done so, you may need to add
> /usr/local/cuda-7.5/lib
> and/or /usr/local/cuda-7.5/lib64 to LD_LIBRARY_PATH using the command
> export LD_LIBRARY_PATH="/usr/local/cuda-7.5/lib:${LD_LIBRARY_PATH}"
> (bash, sh)
> setenv LD_LIBRARY_PATH "/usr/local/cuda-7.5/lib:${LD_LIBRARY_PATH}"
> (tcsh, csh)
>
> --------------------------------------------------------------------------------
>
> The next step is to type 'make install'
>
> Cleaning the src directories. This may take a few moments.
> Configure complete.
> ######
>
> then
>
>
> *export LD_LIBRARY_PATH="/usr/local/cuda-7.5/lib:${LD_LIBRARY_PATH}"*
>
>
> *make install*
>
> last rows of installation
>
> #####
>
> ./cuda/cuda.a -L/usr/local/cuda-7.5/lib64 -L/usr/local/cuda-7.5/lib
> -lcurand -lcufft -lcudart -lstdc++ -L/home/mijiddorj/installs/amber14/lib
> /home/mijiddorj/installs/amber14/lib/libnetcdff.a
> /home/mijiddorj/installs/amber14/lib/libnetcdf.a
> /home/mijiddorj/installs/amber14/lib/libemil.a -lstdc++
> make[3]: Leaving directory `/home/mijiddorj/installs/amber14/src/pmemd/src'
> Installation of pmemd.cuda complete
> make[2]: Leaving directory `/home/mijiddorj/installs/amber14/src/pmemd'
> make[1]: Leaving directory `/home/mijiddorj/installs/amber14/src'
>
> #####
>
>
> Finally,
>
> *make test*
>
> results same as following lines
>
> ....
>
> ./Run.cellulose_nvt: Program error
> make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored)
> cd cellulose/ && ./Run.cellulose_npt SPFP
> /home/mijiddorj/installs/amber14/include/netcdf.mod
> ../../../bin/pmemd.cuda_SPFP: error while loading shared libraries:
> libcurand.so.7.5: cannot open shared object file: No such file or directory
> ./Run.cellulose_npt: Program error
> make[3]: [test.pmemd.cuda.pme.big] Error 1 (ignored)
> make[3]: Leaving directory `/home/mijiddorj/installs/amber14/test/cuda'
> make[2]: Leaving directory `/home/mijiddorj/installs/amber14/test'
> 0 file comparisons passed
> 0 file comparisons failed
> 327 tests experienced errors
> Test log file saved as
>
> /home/mijiddorj/installs/amber14/logs/test_amber_cuda/2015-11-30_23-15-10.log
> No test diffs to save!
> make[1]: Leaving directory `/home/mijiddorj/installs/amber14/test'
>
This indicates that it is still failing to find libcurand.so.7.5 at
runtime. This should have been fixed by adding
/usr/local/cuda-7.5/lib
to LD_LIBRARY_PATH, but it wasn't. What does the following command print
to the screen:
env | grep LD_LIBRARY_PATH
? Do you see a file named libcurand.so.7.5 in
/usr/local/cuda-7.5/lib
? What about
/usr/local/cuda-7.5/lib
64? What shell do you use? Is it bash? Or some c-shell derivative?
This error means one of two things:
1. You did not set the environment variable correctly. This could happen
if you use bash syntax for csh (i.e., export instead of setenv) or
vice-versa. It could also happen if you set the environment variable in a
different shell than you use to run "make test". Adding that command to
your resource file (e.g., ~/.bashrc) will usually ensure that it is set in
every
shell that you open (just remember that modifying .bashrc does not affect
any shells that are already open at the time).
2. The requested library, libcurand.so.7.5, is not actually there.
As many times as I've seen this error on Linux -- and it has been a lot --
the problem has *always* been one of these.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 01 2015 - 05:00:02 PST
