Thanks for creating and maintaining pkdgrav3. I am hoping to run a high-res (~3072^3) dark-matter only simulation with pkdgrav3; such a resolution would not have been possible with (at least my versions of) Gadget3.
On our supercomputer cluster, pkdgrav3 failed to
configure even when the appropriate dependencies were loaded. The reported error was that
gsl could not be found, even though the
gsl module was loaded. We tracked the error down and seemed that the
gsl error was really an
fftw3 error from a previous step.
In any case, the solution we found was to
export CC=mpicc. The final link step failed again but this was because the link step was using
g++; after replacing the final
mpic++, I now have an executable of
For reference, I was running
./configure --with-fftw --with-cuda. I have also tried to run
./configure --with-fftw --with-cuda --with-mpi but both of these fail at the
gsl-config error (if
export CC=mpicc is not active)
I have copy-pasted the error message and attached the
config.log file -- hope that helps. Happy to provide further info.
Thanks again for the software!
checking for fftwf_execute in -lfftw3f... yes checking for fftwf_mpi_init in -lfftw3f_mpi... yes checking for fftwf_init_threads in -lfftw3f_threads... yes checking for gsl-config... /apps/skylake/software/compiler/gcc/6.4.0/gsl/2.4/bin/gsl-config checking for GSL - version >= 1.8... no *** Could not run GSL test program, checking why... *** The test program compiled, but did not run. This usually means *** that the run-time linker is not finding GSL or finding the wrong *** version of GSL. If it is not finding GSL, you'll need to set your *** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point *** to the installed location Also, make sure you have run ldconfig if that *** is required on your system *** *** If you have an old version installed, it is best to remove it, although *** you may also be able to get things to work by modifying LD_LIBRARY_PATH configure: error: Unable to locate GNU Scientific Library (gsl)
[~/research/codes/pkdgrav3 @farnarkle1] module list Currently Loaded Modules: 1) binutils/2.30 6) ifort/2018.1.163-gcc-6.4.0 11) gcc/6.4.0 16) matplotlib/2.2.2-python-3.6.4 21) mpi4py/3.0.0-python-3.6.4 2) szip/2.1.1 7) icc/2018.1.163-gcc-6.4.0 12) openblas/0.2.20 17) openmpi/3.0.0 22) h5py/2.7.1-python-3.6.4 3) nvidia/.384.90 (H,S) 8) git/2.16.0 13) gsl/2.4 18) fftw/3.3.7 4) slurm/.latest (H,S) 9) cuda/9.0.176 14) sqlite/3.21.0 19) hdf5/1.10.1 5) intel/2018.1.163-gcc-6.4.0 10) gcccore/6.4.0 15) python/3.6.4 20) scalapack/2.0.2-openblas-0.2.20 Where: S: Module is Sticky, requires --force to unload or purge H: Hidden Module