It turns out that the solution was quite simple: I was using Intel’s compiler, so I need to change “gfortran” to “ifcore” in build.conf.
That combined with Michael’s advice got things working. -Leon From: Kwant-discuss <kwant-discuss-boun...@kwant-project.org<mailto:kwant-discuss-boun...@kwant-project.org>> on behalf of "Leon Maurer (lmaurer)" <lmau...@sandia.gov<mailto:lmau...@sandia.gov>> Date: Friday, October 7, 2016 at 9:10 AM To: "kwant-discuss@kwant-project.org<mailto:kwant-discuss@kwant-project.org>" <kwant-discuss@kwant-project.org<mailto:kwant-discuss@kwant-project.org>> Subject: Re: [Kwant] [EXTERNAL] Re: more MUMPS problems Hello Michael, I’ve tried adding the new libraries, and now I have a slightly different error: ImportError: /ascldap/users/lmaurer/local/lib/python3.5/site-packages/kwant-1.2.2-py3.5-linux-x86_64.egg/kwant/linalg/_mumps.cpython-35m-x86_64-linux-gnu.so: undefined symbol: for_close Previously, the undefined symbol was “__kmpc_ok_to_fork”. I guess that’s progress! Any more advice? -Leon From: Kwant-discuss <kwant-discuss-boun...@kwant-project.org<mailto:kwant-discuss-boun...@kwant-project.org>> on behalf of Michael Wimmer <m.t.wim...@tudelft.nl<mailto:m.t.wim...@tudelft.nl>> Date: Friday, October 7, 2016 at 12:01 AM To: "kwant-discuss@kwant-project.org<mailto:kwant-discuss@kwant-project.org>" <kwant-discuss@kwant-project.org<mailto:kwant-discuss@kwant-project.org>> Subject: [EXTERNAL] Re: [Kwant] more MUMPS problems Dear Leon, Try the following: In the libraries line with the mkl limbs, add iomp5 pthread The errors that you see refer to that the openmp library is missing. Alternatively you could try to use anaconda (search previous emails on this list for details) Best, Michael Von meinem iPad gesendet Am 06.10.2016 um 23:12 schrieb Maurer, Leon <lmau...@sandia.gov<mailto:lmau...@sandia.gov>>: Hello everyone, I’m in the unfortunate position of having to compile Kwant (and all of its dependencies) from scratch in my home folder, and I’m having trouble getting Kwant to play well with MUMPS. After quite a bit of futzing, I’ve got everything to compile happily (the Kwant build recognizes the "User-configured MUMPS”), but Kwant still won’t work with MUMPS at runtime: ############################# In [1]: import kwant /home/lmaurer/local/lib/python3.5/site-packages/kwant-1.2.2-py3.5-linux-x86_64.egg/kwant/solvers/default.py:18: RuntimeWarning: MUMPS is not available, SciPy built-in solver will be used as a fallback. Performance can be very poor in this case. "Performance can be very poor in this case.", RuntimeWarning) In [2]: from kwant.linalg import mumps --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-2-2962310cb52c> in <module>() ----> 1 from kwant.linalg import mumps /home/lmaurer/local/lib/python3.5/site-packages/kwant-1.2.2-py3.5-linux-x86_64.egg/kwant/linalg/mumps.py in <module>() 15 import numpy as np 16 import scipy.sparse ---> 17 from . import _mumps 18 from .fortran_helpers import prepare_for_fortran 19 ImportError: /home/lmaurer/local/lib/python3.5/site-packages/kwant-1.2.2-py3.5-linux-x86_64.egg/kwant/linalg/_mumps.cpython-35m-x86_64-linux-gnu.so: undefined symbol: __kmpc_ok_to_fork ############################# For what it’s worth, I’ve put my entire build process below. It’s probably too much information, but the short version is that I’m using Intel’s complier on Linux. The Kwant-specific stuff is near the end. The earlier stuff is compiling Python, SCOTCH, METIS, and MUMPS. Any advice? Thanks. -Leon # folders to hold everything cd mkdir local mkdir build cd build # install python and packages wget https://www.python.org/ftp/python/3.5.2/Python-3.5.2.tar.xz tar xf Python-3.5.2.tar.xz cd Python-3.5.2 ./configure --prefix=~/local make make install export PATH=~/local/bin:$PATH cd .. # install important python packages pip3 install scipy tinyarray matplotlib cython # get SCOTCH, METIS, MUMPS wget http://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz wget http://graal.ens-lyon.fr/MUMPS/MUMPS_5.0.2.tar.gz tar xf scotch_6.0.4.tar.gz tar xf metis-5.1.0.tar.gz tar xf MUMPS_5.0.2.tar.gz # install METIS cd metis-5.1.0 make config shared=1 prefix=~/local/ make make install cd .. # install SCOTCH cd scotch_6.0.4/src/ cp Make.inc/Makefile.inc.x86-64_pc_linux2.icc Makefile.inc # need to tweak the makefile nano Makefile.inc Add "-fPIC” to the line that starts with "CFLAGS" make make esmumps make install prefix=~/local # make install won't install esmumps... copy files manually cd ../.. cp scotch_6.0.4/lib/libesmumps.a ~/local/lib/ cp scotch_6.0.4/include/esmumps.h ~/local/include/ # install MUMPS cd MUMPS_5.0.2 cp Make.inc/Makefile.INTEL.SEQ Makefile.inc # need to make a bunch of changes to Makefile.inc nano Makefile.inc 1) change "#SCOTCHDIR = ${HOME}/scotch_6.0" to "SCOTCHDIR = ${HOME}/local/lib" 2) uncomment the line "LSCOTCH = -L$(SCOTCHDIR)/lib -lesmumps -lscotch -lscotcherr" 3) change the line "#LMETISDIR = /local/metis/" to "LMETISDIR = ${HOME}/local/lib" 4) uncomment the line "LMETIS = -L$(LMETISDIR) -lmetis" 5) change the line "ORDERINGSF = -Dpord" to "ORDERINGSF = -Dpord -Dscotch -Dmetis" 6) change "MKLROOT=/opt/intel/mkl/lib/intel64" to "MKLROOT=/opt/intel-12.1/mkl/lib/intel64" 7) add the "-fPIC" compiler flag to the lines that begin "OPTF", "OPTL", and "OPTC" # about damn time! make z # there's no automatic installation... cp include/* ~/local/include/ cp lib/* ~/local/lib/ cp libseq/libmpiseq.a ~/local/lib/ cp libseq/*.h ~/local/include/ cd .. # now for kwant git clone --branch v1.2.2 http://gitlab.kwant-project.org/kwant/kwant.git cd kwant # need to make a new configuration file nano build.conf #### START OF FILE [lapack] libraries = mkl_intel_lp64 mkl_sequential mkl_core mkl_def library_dirs = /opt/intel-12.1/mkl/lib/intel64 extra_link_args = -Wl,-rpath=/opt/intel-12.1/mkl/lib/intel64 [mumps] libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran library_dirs = /home/lmaurer/local/lib/ include_dirs = /home/lmaurer/local/include #### END OF FILE # finally make and install kwant python3 setup.py build python3 setup.py install # need to do the following or kwant won't be able to find libmetis.so export LD_LIBRARY_PATH=~/local/lib/:$LD_LIBRARY_PATH For reference, here are my libs and headers $ ls local/lib/ libesmumps.a libmpiseq.a libpord.a libscotch.a libscotcherrexit.a libzmumps.a python3.5 libmetis.so libmumps_common.a libpython3.5m.a libscotcherr.a libscotchmetis.a pkgconfig $ ls local/include/ cmumps_c.h cmumps_struc.h dmumps_root.h elapse.h metis.h mpi.h mumps_c_types.h scotchf.h smumps_c.h smumps_struc.h zmumps_root.h cmumps_root.h dmumps_c.h dmumps_struc.h esmumps.h mpif.h mumps_compat.h python3.5m scotch.h smumps_root.h zmumps_c.h zmumps_struc.h
