I’m having an issue running Haddock3.0 on a particular compute cluster. When running I receive the following error on the first step:
haddock.core.exceptions.CNSRunningError: b’/gpfs/u/scratch/CLVL/CLVLwrtn/haddock3/bin/cns: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory\n’
Some background: gfortran is being loaded as a module, and therefore libgfortran.so.5 is not in /usr/lib64. The “standard” gfortran would be fine (it runs fine on the login node), but the compute nodes cannot see everything in /usr/lib64 for some reason (including libgfortran.so.3 for gcc 4.8.5).
The folder containing libgfortran.so.5 is in my library path, so I can’t sort why I’m having the issue. Any help is appreciated.
Some background: gfortran is being loaded as a module, and therefore libgfortran.so.5 is not in /usr/lib64. The “standard” gfortran would be fine (it runs fine on the login node), but the compute nodes cannot see everything in /usr/lib64 for some reason (including libgfortran.so.3 for gcc 4.8.5).
I assume you tried to load the module on the nodes as well?
Did you try to compile CNS with the -static-libgfortran option?
E.g. in the Makefile for the load library options:
# link options
LD = gfortran
LDFLAGS = -w $(EXT_LDFLAGS) -static-libgfortran
Yeah, the module is loaded. I gave the -static-libgfortran flag a shot to no avail.
edit Ignore the above. I edited the wrong Makefile; appears to be working now, thanks!
Drop me an email and I will share a CNS executable (statically compiled).
I assume you are running on Linux?
Sorry, I should have just edited the first sentence out. I initially modified the gfortran_mp makefile instead of the gfortran one. Everything is working correctly now.