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| <TableOfContents()> | <<TableOfContents()>> |
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| == MUMPS - direct solver for real and complex valued unsymmetric matrices == |
== MUMPS - direct solver for real and complex valued unsymmetric matrices == |
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| === Installing packages in Debian, Ubuntu or Redhat (MPI version) === |
=== Installing packages in Debian, Ubuntu or Redhat (MPI version) === |
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| For the Linux distributions Debian or Ubuntu install the package | For the Linux distributions Debian or Ubuntu install the package {{{libmumps-dev}}} using the packet manager. This package includes the library (installed to where the MPI libraries are installed, type {{{locate libdmumps}}} to find them) and the include files (copied to {{{/usr/include}}}). |
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| <pre>libmumps-dev</pre> | === Installing packages in Debian, Ubuntu or Redhat (sequential version) === |
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| using the packet manager. This package includes the library (installed to where the MPI libraries are installed, type {{{locate libdmumps}}} to find them) and the include files (copied to =/usr/include=). | For the Linux distributions Debian or Ubuntu install the package {{{libmumps-seq-dev}}} using the packet manager. This package includes the library (copied to {{{/usr/lib}}} or {{{/usr/lib64}}}) and the include files (copied to {{{/usr/include/mumps_seq}}}). |
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| === Installing packages in Debian, Ubuntu or Redhat (sequential version) === |
'''Remark''': use this version only if you don't compile with MPI. |
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| For the Linux distributions Debian or Ubuntu install the package <pre>libmumps-seq-dev</pre> using the packet manager. This package includes the library (copied to =/usr/lib= or =/usr/lib64=) and the include files (copied to =/usr/include/mumps_seq=). Known problems * MPI does not compile anymore. This is due to the fact that some partial MPI implementations are in =/usr/include/mumps_seq=. If you want to use the MPI version of MUMPS, install <pre>libmumps-dev</pre> instead. === Direct installation === |
=== Direct installation === |
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| ==== !! BLACS ==== |
==== BLACS ==== |
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| * Download both [http://www.netlib.org/blacs/mpiblacs.tgz Blacs] and [http://www.netlib.org/blacs/mpiblacs-patch03.tgz Blacs patch] and unpack them to =$(CONCEPTS_DEV)/../BLACS=. This can be done also by <pre>cd $(CONCEPTS_DEV)/.. <br />wget http://www.netlib.org/blacs/mpiblacs.tgz <br />tar -xzf mpiblacs.tgz <br />wget http://www.netlib.org/blacs/mpiblacs-patch03.tgz <br />tar -zxf mpiblacs-patch03.tgz <br />cd BLACS</pre> | * Download both [[http://www.netlib.org/blacs/mpiblacs.tgz|Blacs]] and [[http://www.netlib.org/blacs/mpiblacs-patch03.tgz|Blacs patch]] and unpack them to {{{$(CONCEPTS_DEV)/../BLACS}}}. This can be done also by {{{ cd $(CONCEPTS_DEV)/.. wget http://www.netlib.org/blacs/mpiblacs.tgz tar -xzf mpiblacs.tgz wget http://www.netlib.org/blacs/mpiblacs-patch03.tgz tar -zxf mpiblacs-patch03.tgz cd BLACS }}} |
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| <verbatim> MPILIB = -L$(MPILIBdir) -lmpi -lmpi_f77 -lmpi_f90 -lmpi_cxx</verbatim> |
{{{ MPILIB = -L$(MPILIBdir) -lmpi -lmpi_f77 -lmpi_f90 -lmpi_cxx }}} if you're using OpenMPI. |
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| if you're using OpenMPI. You also need to replaces lines 198, 199 and 204 by <verbatim> F77 = gfortran F77NO_OPTFLAGS = -fPIC -I$(MPIINCdir) CCFLAGS = -fPIC -O4 -I$(MPIINCdir)</verbatim> |
You also need to replaces lines 198, 199 and 204 by {{{ F77 = gfortran F77NO_OPTFLAGS = -fPIC -I$(MPIINCdir) CCFLAGS = -fPIC -O4 -I$(MPIINCdir) }}} |
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| ==== !! !ScaLAPACK ==== |
==== ScaLAPACK ==== |
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| The !ScaLAPACK (Scalable Linear Algebra PACKage) is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. | The ScaLAPACK (Scalable Linear Algebra PACKage) is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. |
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| * Download [http://www.netlib.org/scalapack/scalapack-2.0.2.tgz Scalapack] and unpack it to =$(CONCEPTS_DEV)/../scalapack-2.0.2=. This can be done also by <pre>cd $(CONCEPTS_DEV)/.. <br />wget http://www.netlib.org/scalapack/scalapack-2.0.2.tgz <br />tar -xzf scalapack-2.0.2.tgz <br />cd scalapack-2.0.2</pre> | * Download [[http://www.netlib.org/scalapack/scalapack-2.0.2.tgz|Scalapack]] and unpack it to {{{$(CONCEPTS_DEV)/../scalapack-2.0.2}}}. This can be done also by {{{ cd $(CONCEPTS_DEV)/.. wget http://www.netlib.org/scalapack/scalapack-2.0.2.tgz tar -xzf scalapack-2.0.2.tgz cd scalapack-2.0.2 }}} |
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| * Run the configuration tool, typing {{{ccmake .}}}. Activate advanced editing (with key 't'), and edit both {{{CMAKE_C_FLAGS}}} and {{{CMAKE_FORTRAN_FLAGS}}} to add =-fPIC=., then press 'c' to run configuration script, and 'g' to generate and exit. | * Run the configuration tool, typing {{{ccmake .}}}. Activate advanced editing (with key 't'), and edit both {{{CMAKE_C_FLAGS}}} and {{{CMAKE_FORTRAN_FLAGS}}} to add {{{-fPIC}}}, then press 'c' to run configuration script, and 'g' to generate and exit. |
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| * Modify the flag in =$(CONCEPTS_DEV)/boost-build-modules.jam=, to put <pre>SCALAPACK_PATH = $(CONCEPTS_DEV)/../scalapack-2.0.2/lib</pre> | * Modify the flag in {{{$(CONCEPTS_DEV)/boost-build-modules.jam}}}, to put {{{SCALAPACK_PATH = $(CONCEPTS_DEV)/../scalapack-2.0.2/lib}}}. |
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| ==== !! MUMPS ==== |
==== MUMPS ==== |
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| http://graal.ens-lyon.fr/MUMPS (MUltifrontal Massively Parallel sparse direct Solver) is a massively parallel solver mainly developed at ENS Lyon. | MUMPS (MUltifrontal Massively Parallel sparse direct Solver) is a massively parallel solver mainly developed at [[http://graal.ens-lyon.fr/MUMPS|ENS Lyon]]. |
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| * Request ["http://graal.ens-lyon.fr/MUMPS/index.php?page=dwnld||here"] for downloading the library. * Get the file {{{MUMPS_x.xx.x.tar.gz}}} using the download link provided in your mail (in our example, {{{MUMPS-5.1.1.tar.gz}}}) and copy it to the same root folder as BLACS and ScaLAPACK, i.e. =$(CONCEPTS_DEV)/..=). |
* Request [[http://graal.ens-lyon.fr/MUMPS/index.php?page=dwnld|here]] for downloading the library. * Get the file {{{MUMPS_x.xx.x.tar.gz}}} using the download link provided in your mail (in our example, {{{MUMPS-5.1.1.tar.gz}}}) and copy it to the same root folder as BLACS and ScaLAPACK, i.e. {{{$(CONCEPTS_DEV)/..}}}). |
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| <verbatim> | {{{ |
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| > OPTL = -fPIC -O</verbatim> | > OPTL = -fPIC -O }}} |
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| * Modify the flag in =$(CONCEPTS_DEV)/boost-build-modules.jam=, to put <pre>MUMPS_PATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/lib</pre> and <pre>MUMPS_INCLPATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/include</pre> | * Modify the flag in {{{$(CONCEPTS_DEV)/boost-build-modules.jam}}}, to put {{{MUMPS_PATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/lib}}} and {{{MUMPS_INCLPATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/include}}}. |
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| == Umfpack - direct solver for real valued unsymmetric matrices == |
== Umfpack - direct solver for real valued unsymmetric matrices == |
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| <verbatim> gcc.compile.c++ builds/operator/gcc-4/debug/umfpack.o operator/umfpack.cc:9:23: error: umfpack.h: No such file or directory </verbatim> |
{{{ gcc.compile.c++ builds/operator/gcc-4/debug/umfpack.o operator/umfpack.cc:9:23: error: umfpack.h: No such file or directory }}} |
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| '''Important:''' Make sure that the libraries {{{libamd.so}}}, {{{libcamd.so}}}, {{{libcolamd.so}}}, {{{libccolamd.so}}}, {{{libcolord.so}}}, {{{libcholmod.so}}} and {{{libsuitesparseconfig.so}}} are installed into =/usr/lib= or =/usr/lib64=. Otherwise specify the path {{{UMFPACK_PATH}}} in =$(CONCEPTS_DEV)/boost-build-modules.jam=. Furthermore, make sure that the include file {{{umfpack.h}}} is located in =/usr/include=, =/usr/include/ufpack=, or =/usr/include/suitespare=. Otherwise specify the include path {{{UMFPACK_INCLPATH}}} in =$(CONCEPTS_DEV)/boost-build-modules.jam=. Note that the libraries need to have exactly the name as given above. If they should have a suffix with the version number for example, you have to create symbolic links. | '''Important:''' Make sure that the libraries {{{libamd.so}}}, {{{libcamd.so}}}, {{{libcolamd.so}}}, {{{libccolamd.so}}}, {{{libcolord.so}}}, {{{libcholmod.so}}} and {{{libsuitesparseconfig.so}}} are installed into {{{/usr/lib}}} or {{{/usr/lib64}}}. Otherwise specify the path {{{UMFPACK_PATH}}} in {{{$(CONCEPTS_DEV)/boost-build-modules.jam}}}. Furthermore, make sure that the include file {{{umfpack.h}}} is located in {{{/usr/include}}}, {{{/usr/include/umfpack}}}, or {{{/usr/include/suitespare}}}. Otherwise specify the include path {{{UMFPACK_INCLPATH}}} in {{{$(CONCEPTS_DEV)/boost-build-modules.jam}}}. Note that the libraries need to have exactly the name as given above. If they should have a suffix with the version number for example, you have to create symbolic links. |
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| == !SuperLU - direct solver for real and complex valued unsymmetric matrices == |
== SuperLU - direct solver for real and complex valued unsymmetric matrices == |
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| === Installing packages in Debian, Ubuntu or Redhat === |
=== Installing packages in Debian, Ubuntu or Redhat === |
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| For the Linux distributions Debian or Ubuntu install the package {{{libsuperlu3-dev}}}, or any higher version, using your packet manager. This package includes the library (installed to =/usr/lib= or =/usr/lib64=) and the include files (copied to =/usr/include= or =/usr/include/superlu=). | For the Linux distributions Debian or Ubuntu install the package {{{libsuperlu3-dev}}}, or any higher version, using your packet manager. This package includes the library (installed to {{{/usr/lib}}} or {{{/usr/lib64}}}) and the include files (copied to {{{/usr/include}}} or {{{/usr/include/superlu}}}). |
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| The !SuperLU packages (RPM) for Redhat includes the library and includes files as well. | The SuperLU packages (RPM) for Redhat includes the library and includes files as well. |
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| === Direct installation === |
=== Direct installation === |
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| * Download [http://crd.lbl.gov/~xiaoye/SuperLU/superlu_3.1.tar.gz SuperLU 3.1] and unpack it to =/scratch/kersten/SuperLU= (when Concepts is for example in =/scratch/kersten/concepts-2=). This can be done also by <pre>cd /scratch/kersten <br />wget http://crd.lbl.gov/~xiaoye/SuperLU/superlu_3.1.tar.gz <br />tar -xzf superlu_3.1.tar.gz <br />mv SuperLU_3.1 SuperLU <br />cd SuperLU</pre> * Copy the file [https://wiki.math.ethz.ch/pub/Concepts/InstallationGuide/make.inc make.inc] into =/scratch/kersten/SuperLU= |
* Download [[http://crd.lbl.gov/~xiaoye/SuperLU/superlu_3.1.tar.gz|SuperLU 3.1]] and unpack it to {{{/scratch/kersten/SuperLU}}} (when Concepts is for example in {{{/scratch/kersten/concepts-2}}}). This can be done also by {{{ cd /scratch/kersten wget http://crd.lbl.gov/~xiaoye/SuperLU/superlu_3.1.tar.gz tar -xzf superlu_3.1.tar.gz <br />mv SuperLU_3.1 SuperLU cd SuperLU }}} * Copy the file [[Concepts/SuperLU/make.inc|make.inc]] into =/scratch/kersten/SuperLU= |
Installation guide : direct solver
Contents
MUMPS - direct solver for real and complex valued unsymmetric matrices
Installing packages in Debian, Ubuntu or Redhat (MPI version)
For the Linux distributions Debian or Ubuntu install the package libmumps-dev using the packet manager. This package includes the library (installed to where the MPI libraries are installed, type locate libdmumps to find them) and the include files (copied to /usr/include).
Installing packages in Debian, Ubuntu or Redhat (sequential version)
For the Linux distributions Debian or Ubuntu install the package libmumps-seq-dev using the packet manager. This package includes the library (copied to /usr/lib or /usr/lib64) and the include files (copied to /usr/include/mumps_seq).
Remark: use this version only if you don't compile with MPI.
Direct installation
If your Linux distribution is not able to install Debian or RPM packages follow this guide to install the library yourself.
BLACS
The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. It's used by Scalapack.
Download both Blacs and Blacs patch and unpack them to $(CONCEPTS_DEV)/../BLACS. This can be done also by
cd $(CONCEPTS_DEV)/.. wget http://www.netlib.org/blacs/mpiblacs.tgz tar -xzf mpiblacs.tgz wget http://www.netlib.org/blacs/mpiblacs-patch03.tgz tar -zxf mpiblacs-patch03.tgz cd BLACS
Copy the file BMAKES/Bmake.MPI-LINUX into Bmake.inc and edit it. You need to change lines 50 ( MPIdir) to precise where your MPI installation is, and you need to replace line 53 ( MPILIB) by
MPILIB = -L$(MPILIBdir) -lmpi -lmpi_f77 -lmpi_f90 -lmpi_cxx
if you're using OpenMPI.You also need to replaces lines 198, 199 and 204 byF77 = gfortran F77NO_OPTFLAGS = -fPIC -I$(MPIINCdir) CCFLAGS = -fPIC -O4 -I$(MPIINCdir)
Compile the library typing make mpi
ScaLAPACK
The ScaLAPACK (Scalable Linear Algebra PACKage) is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems.
Download Scalapack and unpack it to $(CONCEPTS_DEV)/../scalapack-2.0.2. This can be done also by
cd $(CONCEPTS_DEV)/.. wget http://www.netlib.org/scalapack/scalapack-2.0.2.tgz tar -xzf scalapack-2.0.2.tgz cd scalapack-2.0.2
Run the configuration tool, typing ccmake .. Activate advanced editing (with key 't'), and edit both CMAKE_C_FLAGS and CMAKE_FORTRAN_FLAGS to add -fPIC, then press 'c' to run configuration script, and 'g' to generate and exit.
Compile it, typing make scalapack.
Modify the flag in $(CONCEPTS_DEV)/boost-build-modules.jam, to put SCALAPACK_PATH = $(CONCEPTS_DEV)/../scalapack-2.0.2/lib.
MUMPS
MUMPS (MUltifrontal Massively Parallel sparse direct Solver) is a massively parallel solver mainly developed at ENS Lyon.
Request here for downloading the library.
Get the file MUMPS_x.xx.x.tar.gz using the download link provided in your mail (in our example, MUMPS-5.1.1.tar.gz) and copy it to the same root folder as BLACS and ScaLAPACK, i.e. $(CONCEPTS_DEV)/..).
Unpack it using tar -zxf MUMPS-5.1.1.tar.gz, and go inside folder MUMPS-5.1.1
Copy the file Make.inc/Makefile.inc.generic into Makefile.inc and edit it. For example, here is the difference between the Make.inc/Makefile.inc.generic and the modified version Makefile.inc
94c94 < CC = cc --- > CC = gcc 96c96 < FC = f90 --- > FC = gfortran 98c98 < FL = f90 --- > FL = gfortran 108c108 < SCALAP = -lscalapack -lblacs --- > SCALAP = -L$(CONCEPTS_DEV)/../scalapack-2.0.2/lib -lscalapack $(CONCEPTS_DEV)/../BLACS/LIB/blacs_MPI-LINUX-0.a $(CONCEPTS_DEV)/../BLACS/LIB/blacsF77init_MPI-LINUX-0.a $(CONCEPTS_DEV)/../BLACS/LIB/blacsCinit_MPI-LINUX-0.a 111c111 < INCPAR = -I/usr/include --- > INCPAR = -I/usr/mpi/gcc/openmpi-1.4.2/include 114c114 < LIBPAR = $(SCALAP) -L/usr/lib -lmpi --- > LIBPAR = $(SCALAP) -L/usr/mpi/gcc/openmpi-1.4.2/lib64 -lmpi 143,145c143,145 < OPTF = -O < OPTC = -O -I. < OPTL = -O --- > OPTF = -fPIC -O > OPTC = -fPIC -O -I. > OPTL = -fPIC -O
Compile using make alllib.
Modify the flag in $(CONCEPTS_DEV)/boost-build-modules.jam, to put MUMPS_PATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/lib and MUMPS_INCLPATH = $(CONCEPTS_DEV)/../MUMPS-5.0.2/include.
Umfpack - direct solver for real valued unsymmetric matrices
Umfpack is a direct solver for real and complex matrices, however only the interface to routines for real matrices is implemented (version ≥ 4.1). Ubuntu or Debian:
Install the package libsuitesparse-dev. If only the package libsuitesparse is installed, the package will not be found creating an error like
gcc.compile.c++ builds/operator/gcc-4/debug/umfpack.o operator/umfpack.cc:9:23: error: umfpack.h: No such file or directory
Important: Make sure that the libraries libamd.so, libcamd.so, libcolamd.so, libccolamd.so, libcolord.so, libcholmod.so and libsuitesparseconfig.so are installed into /usr/lib or /usr/lib64. Otherwise specify the path UMFPACK_PATH in $(CONCEPTS_DEV)/boost-build-modules.jam. Furthermore, make sure that the include file umfpack.h is located in /usr/include, /usr/include/umfpack, or /usr/include/suitespare. Otherwise specify the include path UMFPACK_INCLPATH in $(CONCEPTS_DEV)/boost-build-modules.jam. Note that the libraries need to have exactly the name as given above. If they should have a suffix with the version number for example, you have to create symbolic links.
SuperLU - direct solver for real and complex valued unsymmetric matrices
Installing packages in Debian, Ubuntu or Redhat
For the Linux distributions Debian or Ubuntu install the package libsuperlu3-dev, or any higher version, using your packet manager. This package includes the library (installed to /usr/lib or /usr/lib64) and the include files (copied to /usr/include or /usr/include/superlu).
The SuperLU packages (RPM) for Redhat includes the library and includes files as well.
Direct installation
If your Linux distribution is not able to install Debian or RPM packages follow this guide to install the library yourself. The guide refers to installing !SuperLU of version 3.1 but it can easily be adjusted for any other version.
Download SuperLU 3.1 and unpack it to /scratch/kersten/SuperLU (when Concepts is for example in /scratch/kersten/concepts-2). This can be done also by
cd /scratch/kersten wget http://crd.lbl.gov/~xiaoye/SuperLU/superlu_3.1.tar.gz tar -xzf superlu_3.1.tar.gz <br />mv SuperLU_3.1 SuperLU cd SuperLU
Copy the file make.inc into =/scratch/kersten/SuperLU=
If your gcc is 4.xx or newer you have to edit make.inc and use something like <pre>SuperLUroot = /scratch/kersten/SuperLU_3.1 <br />SUPERLULIB = $(SuperLUroot)/libsuperlu.a <br />BLASLIB = /usr/lib/libblas.a <br />TMGLIB = libtmglib.a <br />LIBS = $(SUPERLULIB) $(BLASLIB) <br />CC = gcc-3.4.2 <br />CFLAGS = -O3 -fPIC -fomit-frame-pointer -g <br />FORTRAN = gfortran <br />FFLAGS = -O -fPIC <br />LOADER = gcc-3.4.2 <br />LOADOPTS = -O3 -fPIC </pre>
Change in the file =/scratch/kersten/SuperLU/SRC/Makefile= <pre>superlu_timer.o: superlu_timer.c ; $(CC) -c $(NOOPTS) $<</pre> into <pre>superlu_timer.o: superlu_timer.c ; $(CC) -c $(NOOPTS) -fPIC $< </pre>
execute in =/scratch/kersten/SuperLU= <pre>make</pre>
When building Concepts (call of bjam) it indicates, that it finds !SuperLU with the line <pre>* Activating support for direct solver SuperLU.</pre>
Known problems
Pre-installed BLAS in =/usr/lib/libblas.a= <pre>/scratch/kersten/SuperLU/lib/libsuperlu_3.1.a(xerbla.o):/scratch/kersten/SuperLU/SRC/xerbla.c:5: first defined here /usr/bin/ld: Warning: size of symbol `xerbla_' changed from 30 in /scratch/kersten/SuperLU/lib/libsuperlu_3.1.a(xerbla.o) to 38 in /usr/lib/libblas.a(xerbla.o)</pre> Solution: deactive xerbla.o in SRC/Makefile by changing <pre>LAAUX = lsame.o</pre> into <pre>LAAUX = lsame.o #xerbla.o</pre>