Hi Everyone,
I have been trying to install deal.ii on NERSC Cori cluster
for use on the KNL compute nodes using the following procedure :
Clone and setup :
*git clone --single-branch --branch dealii-9.1 *
*https://github.com/dealii/dealii.git*
<https://github.com/dealii/dealii.git>
*mkdir build*
*mkdir dealii_trial*
*cd build *
Build and install on an interactive node :
*cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc
-DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn -DDEAL_II_WITH_MPI=ON
-DDEAL_II_WITH_PETSC=ON -DDEAL_II_WITH_P4EST=ON
-DDEAL_II_WITH_LAPACK=ON
-DCMAKE_INSTALL_PREFIX=/global/project/projectdirs/m2360/packagesCPFE/dealii_trial/
../dealii*
which completes without any issues after which
*make -j 32 install*
eventually yields the following error :
--------------------------------------------------------------------------
[ 27%] Building CXX object
bundled/umfpack/AMD/Source/CMakeFiles/obj_amd_long_debug.dir/amd_defaults.cc.o
/bin/sh: expand_instantiations: command not found
make[2]: ***
[source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91:
source/numerics/data_out_dof_data.inst] Error 127
make[2]: *** Waiting for unfinished jobs....
---------------------------------------------------------------------------
Details on procedure before cloning deal.ii are included below :
(i) I first loaded the necessary modules so that *module list* displayed
Currently Loaded Modulefiles:
1)
modules/3.2.11.4 16)
rca/2.2.20-7.0.1.1_4.46__g8e3fb5b.ari
2)
altd/2.0
17)
atp/2.1.3
3)
darshan/3.1.7 18)
PrgEnv-intel/6.0.5
4)
intel/19.0.3.199 19)
craype-mic-knl
5) craype-network-aries 20)
cray-mpich/7.7.14
6)
craype/2.6.2 21)
craype-hugepages2M
7) udreg/2.3.2-7.0.1.1_3.31__g8175d3d.ari 22) valgrind/3.15.0
8) ugni/6.0.14.0-7.0.1.1_7.33__ge78e5b0.ari 23) zlib/1.2.11
9)
pmi/5.0.14 24)
metis/5.1.0
10) dmapp/7.1.1-7.0.1.1_4.48__g38cf134.ari 25) parmetis/4.0.3
11) gni-headers/5.0.12.0-7.0.1.1_6.28__g3b1768f.ari 26) superlu-dist/6.1.1
12) xpmem/2.2.20-7.0.1.1_4.10__g0475745.ari 27) hypre/2.15.1
13) job/2.2.4-7.0.1.1_3.36__g36b56f4.ari 28)
cmake/3.14.4
14) dvs/2.12_2.2.156-7.0.1.1_8.9__g5aab709e 29)
cray-hdf5/1.10.2.0
15) alps/6.6.58-7.0.1.1_6.4__g437d88db.ari 30)
petsc-real-64/3.11.2
(ii) Set environment variables for dynamic linking
*export XTPE_LINK_TYPE=dynamic*
*export CRAYPE_LINK_TYPE=dynamic*
(iii) p4est installation
*./configure --prefix=/global/project/projectdirs/m2360/packagesCPFE/p4est
--host=x86_64 --enable-vtk-zlib=yes --enable-mpi=yes F77=ftn FC=ftn CC=cc
CXX=CC*
*make -j 32*
*make -j 32 install *
*export P4EST_DIR=/global/project/projectdirs/m2360/packagesCPFE/p4est*
I did initially submit a ticket on NERSC support for assistance with the
installation process and after a few iterations, the person(
https://github.com/JBlaschke) helping me out asked me to contact the
developers. I would really appreciate your help on this.
Thank you.
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
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