Reply To: unable to propagate location of libraries to scons for Rosetta 3.1 [FIXED…SORT OF…]

[Anonymous]

Thanks a lot for the quick response.

Yes, I had tried it on a fresh rosetta_source, but it gave the same result as above. I copied the site.settings.topsail to site.settings (also replaced “INCLUDE” by “C_INCLUDE_PATH”, since I do not have a INCLUDE environment variable, but my C_INCLUDE_PATH has all the INCLUDE paths defined by the modules). See the attached site.settings

The result is the same :
$ ./scons.py bin
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/rap/eer-775-aa/rosetta-3.1/rosetta_source/src/pilot_apps.src.settings”, “/rap/eer-775-aa/rosetta-3.1/rosetta_source/src/pilot_apps.src.settings.template”)
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/debug/linux/2.6/64/x86/gcc/apps/public/AbinitioRelax.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -O0 -g -ggdb -ffloat-store -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -I/software/base-gcc/include -I/software/gmp-4.3.1_gcc/include -I/software/mpfr-2.4.1_gcc/include -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/AbinitioRelax.cc
/software/gcc-4.4.2/libexec/gcc/x86_64-unknown-linux-gnu/4.4.2/cc1plus: error while loading shared libraries: libmpfr.so.1: cannot open shared object file: No such file or directory
scons: *** [build/src/debug/linux/2.6/64/x86/gcc/apps/public/AbinitioRelax.o] Error 1
scons: building terminated because of errors.

As additional information regarding my cluster module settings:

$ module list
No Modulefiles Currently Loaded.
$ module avail

---

/clumeq/Modules/versions

---

3.2.7

---

/clumeq/Modules/modulefiles

---

apps/abaqus-6.9-1 blas-libs/lapack/3.2.1_gcc misc-libs/libpng/1.2.42
apps/ansys-12.1-cfx blas-libs/mkl/10.2.2.025 misc-libs/libpng/1.4.0
apps/ansys-12.1-fluent compilers/gcc/4.4.2 misc-libs/matplotlib/1.0.0_intel
apps/cp2k/2_1-branch compilers/gcc/4.4.2+g77 misc-libs/mpfr/4.3.1_gcc
apps/espresso-4.1.3 compilers/intel/11.1.059 misc-libs/netcdf/3.6.3_intel
apps/flex-2.5.35 compilers/sunstudio/12.1 misc-libs/netcdf/4.1.1_intel
apps/geant-4.9.3 java/jdk1.6.0 misc-libs/netcdf-4.0.1
apps/gpaw/0.7.2 lapack misc-libs/numpy/1.4.1_intel
apps/grass-gis-6.4.0 misc-libs/ParMetis/3.1.1_gcc misc-libs/petsc/2.3.3-p15
apps/gromacs/4.5.1_intel misc-libs/SuperLU/2.3.a_gcc+atlas misc-libs/petsc/3.1-p4
apps/gromacs-4.0.7 misc-libs/SuperLU/4.0_gcc misc-libs/scipy/0.8.0_intel
apps/lammps/3Dec10 misc-libs/SuperLU/DIST-2.3.a_gcc misc-libs/szip-2.1
apps/lammps-30Mar10 misc-libs/ase/3.4.1 mono-2.6.1
apps/namd/2.7b4 misc-libs/boost/1.44.0_intel mpi/openmpi/1.3.4_gcc
apps/octave-3.2.4 misc-libs/charm/6.2.2_intel mpi/openmpi/1.3.4_intel
apps/ox-console/5.10 misc-libs/clhep-2.0.4.3 mpi/openmpi/1.3.4_sunstudio
apps/powerflow-4.1c misc-libs/clhep-2.0.4.5 mpi/openmpi/1.4.1_gcc
apps/powerflow-4.2b misc-libs/fftw/2.1.5 mpi/openmpi/1.4.3_gcc
apps/python-2.6.4 misc-libs/fftw/2.1.5_intel mpi/openmpi/1.4.3_intel
apps/r-2.10.1 misc-libs/fftw/3.2.2 tools/gdb/7.1
apps/structure-2.3.3 misc-libs/gmp/4.3.1_gcc tools/pdtoolkit/3.15_gcc
apps/wine-1.2-rc2 misc-libs/gmp/4.3.1_intel tools/tau/2.19_gcc
blas-libs/GotoBlas2 misc-libs/gsl/1.14_intel tools/tau/2.19_gcc-ompi
blas-libs/atlas/3.9.20 misc-libs/hdf/hdf4.2r4
$ module load compilers/gcc/4.4.2
$ module list
Currently Loaded Modulefiles:
1) misc-libs/mpfr/4.3.1_gcc 2) misc-libs/gmp/4.3.1_gcc 3) compilers/gcc/4.4.2
$ printenv PATH
/software/gcc-4.4.2/bin:/software/base-gcc/bin:/usr/local/bin:/bin:/usr/bin
$ printenv LD_LIBRARY_PATH
/software/mpfr-2.4.1_gcc/lib:/software/gcc-4.4.2/lib64:/software/gcc-4.4.2/lib:/software/base-gcc/lib:/software/base-gcc/lib64:/software/gmp-4.3.1_gcc//lib
$ printenv C_INCLUDE_PATH
/software/base-gcc/include:/software/gmp-4.3.1_gcc//include:/software/mpfr-2.4.1_gcc/include