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by (17.5k points)

...will depend on the machine of course but we want to share an example here.

A general description is given on the webpage:

by (100 points)
Hi, is a specific version of gengetopt required? I'm struggling to compile the laterst version on an HPC, so that I can compile OpenCARP. Thanks.
by (17.5k points)
gengetopt doesn't change frequently. The latest version is from May 2019, thus I think any recent version should work. What's the error message?
by (100 points)
Hi Axel,

The error I'm getting is:

g++ -DHAVE_CONFIG_H -I. -I.. -I../gl -I../gl -g -O2 -MT parser.o -MD -MP -MF .deps/parser.Tpo -c -o parser.o

mv -f .deps/parser.Tpo .deps/parser.Po

g++ -DHAVE_CONFIG_H -I. -I.. -I../gl -I../gl -g -O2 -MT scanner.o -MD -MP -MF .deps/scanner.Tpo -c -o scanner.o

scanner.ll:28:20: fatal error: parser.h: No such file or directory

#include "parser.h"

The HPC I'm trying to install it on is:

These are the modules I loaded:

module load cmake/3.6.0
module load intel/compiler/64/2017.2.174
module load intel/mkl/64/2017.2.174
module load intel/mpi/64/2017.2.174
module load gcc/6.3.0/1
module load libcxx/3.4.2/1
module load flex/2.5.37/1
module load bison/2.7/1
by (100 points)
Hi Axel,

quick update: I managed to fix the issue by creating a link from parser.hh to parser.h. So, gengetopt is installed now.

I'm having a different issue, which seems like a compiler version problem:
"mpiicpc -o build/cmdline.o -c -I./src/imps_src -I./src  -std=c++11 -lstdc++ -O2 -g -DHAVE_DLOPEN  -DSOLVE_CURRENT -DWITH_BLAS -D_GNU_SOURCE -DWITH_PARMETIS -I.  -I../../simulator -I../../physics/limpet/src -I../../fem -I../../fem/slimfem/src -I../../physics       -I../../numerics  -I../../param/include  -I/gpfs/home/misc/cmc16/petsc/athena-intel-slim/include -I/gpfs/home/misc/cmc16/petsc/include  -MMD src/
src/ error: a value of type "const char *" cannot be assigned to an entity of type "char *"
    tok = strchr (arg, ',');

src/ error: a value of type "const char *" cannot be assigned to an entity of type "char *"
    tok = strchr (arg, ',');"

Any ideas?
by (17.5k points)
Looks like a compiler issue, indeed.

What worked for us was the intel compiler version 19.1
module load compiler/intel/19.1
Don't know if that's available on your system, though.
by (100 points)
No, but I'll contact the system support and see what they can do.
Thanks, Axel!

1 Answer

0 votes
by (17.5k points)

On bwUniCluster, the following specific steps implementing the general installation instructions are required (description by Claudia Nagel):

  • First, you need to load the necessary modules in your bash_profile. To do so, open your bash_profile with an editor (e.g. vim, nano, ...) in the terminal and insert the following lines:
module load numlib/petsc/3.13.4-gnu-10.2-openmpi-4.0 
module load compiler/intel/19.1
module load devel/cmake/3.18
module load numlib/python_numpy/1.19.1_python_3.8.5_intel_19.1
module load mpi/openmpi/4.0
  • Log out and back in the cluster to make sure the modules get loaded
  • Start with the section "Building openCARP from source" on the openCARP installation webpage. Since you've loaded PETSc in the modules, skip the first entry and start at "git clone"
  • Follow the instructions step by step as they are written on the installation website for openCARP. 
  • For carputils, I used the "Development Installation". You do not need to install the required python packages as they are already there and loaded with the modules command. Then just follow the instructions on the installation page and consider the following points.
  • Export the PATH and the PYTHONPATH in the .bash_profile with the following commands:
export PATH=$PATH:$HOME/carputils/bin
  • When creating the settings.yaml, file make sure to comment out the following lines (with #) as they cause errors:
  • Export the carputils settings also in your bash_profile. Put the settings file in your home directory (where there should also be the openCARP and the carputils folder). Open the .bash_profile again with an editor and add the following lines
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