Hello,<div><br></div><div>I have been trying to compile Gale from the mercurial repos, and I have run into PETSc error troubles when I try to run a multi-processor job with MUMPS.</div><div><br></div><div>Here the processes I have gone through on a Ubuntu 10.04 x64 bit VM:</div>
<div>1) Apt-get'ed libxml2-dev, mpich2 (with the mpd daemon setup), mercurial</div><div><br></div><div>2) Downloaded and installed HDF5 (with no problems)</div><div><br></div><div>3) Downloaded petsc3.0.0-p12, and extracted it to /usr/local/petsc-3.0.0-p12</div>
<div><br></div><div>4) Chown'ed the whole directory and contents to my username</div><div><br></div><div>5) In the petsc folder, ran the following command:</div><div><br></div><div>config/configure.py --download-mumps=1 --download-parmetis=1 --download-scalapack=1 --download-f-blas-lapack=1 --download-blacs=1 --with-shared=1</div>
<div><br></div><div>(Just to note, right after the "Configuring PETSc.." heading, I get this:</div><div><div><br></div><div>/usr/local/petsc-3.0.0-p12/config/BuildSystem/config/compilers.py:7: DeprecationWarning: the sets module is deprecated</div>
<div> import sets</div><div>/usr/local/petsc-3.0.0-p12/config/PETSc/package.py:7: DeprecationWarning: the md5 module is deprecated; use hashlib instead</div><div> import md5</div><div>/usr/local/petsc-3.0.0-p12/config/BuildSystem/script.py:101: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.</div>
<div> import popen2</div></div><div><br></div><div>after which, the compiling and installing of all the requested modules is as normal)</div><div><br></div><div>After all that, it says:</div><div><br></div><div><div>Compilers:</div>
<div> C Compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -g3 </div><div> Fortran Compiler: mpif90 -fPIC -Wall -Wno-unused-variable -g </div><div>Linkers:</div><div> Shared linker: mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -g3 </div>
<div> Dynamic linker: mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -g3 </div><div>PETSc:</div><div> **</div><div> ** Before running "make" your PETSC_ARCH must be specified with:</div><div>
** ** setenv PETSC_ARCH linux-gnu-c-debug (csh/tcsh)</div><div> ** ** PETSC_ARCH=linux-gnu-c-debug; export PETSC_ARCH (sh/bash)</div><div> **</div><div> **</div><div> ** Before running "make" your PETSC_DIR must be specified with:</div>
<div> ** ** setenv PETSC_DIR /usr/local/petsc-3.0.0-p12 (csh/tcsh)</div><div> ** ** PETSC_DIR=/usr/local/petsc-3.0.0-p12; export PETSC_DIR (sh/bash)</div><div> **</div><div> **</div><div> ** Now build the libraries with "make all"</div>
<div> **</div><div> Clanguage: C</div><div> Scalar type:real</div><div>MPI:</div><div> Includes: -I/usr/include/mpich2</div><div> PETSc shared libraries: enabled</div><div> PETSc dynamic libraries: disabled</div><div>
BLAS/LAPACK: -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lflapack -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lfblas</div>
<div>ParMetis:</div><div> Includes: -I/usr/include/mpich2 -I/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/include</div><div> Library: -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lparmetis -lmetis</div>
<div>SCALAPACK:</div><div> Library: -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lscalapack</div><div>blacs:</div><div> Library: -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lblacs</div>
<div>MUMPS:</div><div> Includes: -I/usr/include/mpich2 -I/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/include</div><div> Library: -Wl,-rpath,/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -L/usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord</div>
</div><div><br></div><div><div>6) Put these into my .bashrc</div><div><br></div><div><div>export PETSC_DIR=/usr/local/petsc-3.0.0-p12</div><div>export PETSC_ARCH=linux-gnu-c-debug</div></div></div><div><br></div><div>and then restarted my terminal.</div>
<div><br></div><div>7) Then I ran the "make all test" command, and at the end got this:</div><div><br></div><div><div>Running test examples to verify correct installation</div><div>C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process</div>
<div>C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes</div><div>Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process</div><div>Completed test examples</div>
<div><br></div><div>7) Mercurial'ed the Gale repo into my home directory. </div><div><br></div><div>8) I then ran ./configure.sh, and get:</div><div><br></div><div><div>earthbyte@earthbyte-virtualmachine:~/Programs/gale$ ./configure.sh scons: Reading SConscript files ...</div>
<div>Checking whether the C compiler worksyes</div><div>Checking for package libXML2... yes</div><div>Checking for package MPI... yes</div><div>Checking for package HDF5... yes</div><div>Checking for package PETSc... yes</div>
<div>Checking for package PETScExt... no</div><div><br></div><div>C compiler: 'mpicc'</div><div>C flags: -g -fPIC -Wwrite-strings -Wno-strict-aliasing -g3 -Wall</div><div>C preprocessor: ['DEBUG', 'HAVE_LIBXML2', 'HAVE_MPI', 'HAVE_HDF5', 'HAVE_PETSC']</div>
<div><br></div><div><br></div><div>***************************************</div><div>* Successfully configured. *</div><div>* Now run './scons' to build. *</div><div>***************************************</div>
<div><br></div><div>scons: done reading SConscript files.</div><div>scons: Building targets ...</div><div>scons: `.' is up to date.</div><div>scons: done building targets.</div></div><div><br></div><div>(A side note, is PETScExt needed? I have tried installing it, but it comes up saying some odd things...)</div>
<div><br></div><div>9) I then ran ./scons -j 2, which eventually ends with:</div><div><br></div><div><div>scons: done building targets.</div></div><div><br></div><div>10) Then, if I run:</div><div><br></div><div>build/bin/Gale input/cookbook/yielding.xml -mat_type aijumps -ksp_type pre only -pc_type lu</div>
<div><br></div><div>or:</div><div><br></div><div>mpirun -np 2 build/bin/Gale input/cookbook/yielding.xml -mat_type aijumps -ksp_type pre only -pc_type lu</div><div><br></div><div>or:</div><div><br></div><div><div>build/bin/Gale input/cookbook/yielding.xml -ksp_type pre only -pc_type lu</div>
</div><div><br></div><div>I get major PETSc errors - here is a snapshot:</div><div><br></div><div><div>[0]PETSC ERROR: build/bin/Gale on a linux-gnu named earthbyte-virtualmachine by earthbyte Wed Jun 23 18:09:11 2010</div>
<div>[0]PETSC ERROR: Libraries linked from /usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib</div><div>[0]PETSC ERROR: Configure run at Wed Jun 23 17:21:05 2010</div><div>[0]PETSC ERROR: Configure options --download-mumps=1 --download-parmetis=1 --download-scalapack --download-f-blas-lapack=1 --download-blacs=1 --with-shared=1</div>
<div>[0]PETSC ERROR: ------------------------------------------------------------------------</div><div>[0]PETSC ERROR: MatSetValues() line 900 in src/mat/interface/matrix.c</div><div>[0]PETSC ERROR: --------------------- Error Message ------------------------------------</div>
<div>[0]PETSC ERROR: Object is in wrong state!</div><div>[0]PETSC ERROR: Mat object's type is not set: Argument # 1!</div><div>[0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 12, Tue Mar 16 23:20:08 CDT 2010</div><div>[0]PETSC ERROR: See docs/changes/index.html for recent updates.</div><div>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.</div>
<div>[0]PETSC ERROR: See docs/index.html for manual pages.</div><div>[0]PETSC ERROR: ------------------------------------------------------------------------</div></div><div><br></div><div>this showed up too:</div><div><br>
</div><div><div>[0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message ------------------------------------</div><div>[1]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type</div>
<div> seehttp://<a href="http://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external">www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external</a>!</div><div>[1]PETSC ERROR: Unknown Mat type given: aijumps!</div>
<div>[1]PETSC ERROR: ------------------------------------------------------------------------</div><div>[1]PETSC ERROR: Petsc Release Version 3.0.0, Patch 12, Tue Mar 16 23:20:08 CDT 2010</div><div>[1]PETSC ERROR: See docs/changes/index.html for recent updates.</div>
<div>[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.</div><div>[1]PETSC ERROR: See docs/index.html for manual pages.</div><div>[1]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[1]PETSC ERROR: build/bin/Gale on a linux-gnu named earthbyte-virtualmachine by earthbyte Wed Jun 23 18:09:11 2010</div><div>[1]PETSC ERROR: Libraries linked from /usr/local/petsc-3.0.0-p12/linux-gnu-c-debug/lib</div>
<div>[1]PETSC ERROR: Configure run at Wed Jun 23 17:21:05 2010</div><div>[1]PETSC ERROR: Configure options --download-mumps=1 --download-parmetis=1 --download-scalapack --download-f-blas-lapack=1 --download-blacs=1 --with-shared=1</div>
<div>[1]PETSC ERROR: ------------------------------------------------------------------------</div><div>[1]PETSC ERROR: MatSetType() line 52 in src/mat/interface/matreg.c</div><div>[1]PETSC ERROR: MatSetFromOptions() line 195 in src/mat/utils/gcreate.c</div>
<div>--------------------- Error Message ------------------------------------</div></div><div><br></div><div><br></div><div>Any ideas what is going wrong?</div><br>Kind Regards,<br><br>Luke Mondy<br>
</div>