libscalapack undefined reference

nwilson

ISSM compilation terminates with

CXX main/issm-issm.o


  CXXLD    issm.exe
/usr/bin/ld: /home/natw/code/issm/trunk/externalpackages/petsc/install/lib/libscalapack.a(PB_Cdtypeset.o): undefined reference to symbol 'dsyr2_'
/home/natw/code/issm/trunk/externalpackages/petsc/install/lib/libpetsc.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: ***  Error 1
make: Leaving directory `/home/natw/code/issm/trunk/src/c'
make: ***  Error 1
make: Leaving directory `/home/natw/code/issm/trunk/src'
make: ***  Error 1
make: Leaving directory `/home/natw/code/issm/trunk'

make: *** Error 2

I compiled PETSc 3.5 before with the install-3.5-linux64.sh script in externapackages/petsc - it appeared to go without a hitch. This is on Ubuntu 14.04. The confiiguration file I used is https://gist.github.com/njwilson23/2a0192bf433d58cb6006.

Is this a PETSc or ScaLAPACK problem? Anything I could try to fix this?

Thanks!

mathieumorlighem

Hi,

This symbol is supposed to be defined by the FBLAS in PETSc, can you do

cd $ISSM_DIR/externalpackages/petsc/install/lib

nm libfblas.a

You should get something like

0000000000000000 T dsyr2_

That means that the symbol is defined in libfblas.a.

If this works, can you do

cd $ISSM_DIR/src/c

make V=1

and send us the output?

Thanks

Mathieu

nwilson

Hi Mathieu,

`nm` contains the entry

dsyr2.o:


0000000000000000 T dsyr2_
                 U _GLOBAL_OFFSET_TABLE_
                 U lsame_
                 U xerbla_

Running `make` from src/c returns


$ make V=1
/bin/bash ../../libtool  --tag=CXX   --mode=link g++ -fPIC -g -O2   -o issm.exe main/issm-issm.o ./libISSMCore.la ./libISSMOverload.la ./libISSMModules.la /home/natw/code/issm/trunk/externalpackages/triangle/install/triangle.a -L/home/natw/code/issm/trunk/externalpackages/petsc/install/lib -lpetsc -ldl -lmetis  /home/natw/code/issm/trunk/externalpackages/m1qn3/install/libm1qn3.a /home/natw/code/issm/trunk/externalpackages/m1qn3/install//libddot.a  -L/home/natw/code/issm/trunk/externalpackages/petsc/install//lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis -lzmumps -lmetis   -L/home/natw/code/issm/trunk/externalpackages/petsc/install// -lscalapack             -L/home/natw/code/issm/trunk/externalpackages/mpich/install/lib -lmpich -lmpl   -lpthread -lrt     -L/home/natw/code/issm/trunk/externalpackages/mpich/install/lib -lmpich -lmpl       
libtool: link: g++ -fPIC -g -O2 -o .libs/issm.exe main/issm-issm.o  ./.libs/libISSMCore.so ./.libs/libISSMOverload.so ./.libs/libISSMModules.so /home/natw/code/issm/trunk/externalpackages/triangle/install/triangle.a -L/home/natw/code/issm/trunk/externalpackages/petsc/install/lib -lpetsc -ldl /home/natw/code/issm/trunk/externalpackages/m1qn3/install/libm1qn3.a /home/natw/code/issm/trunk/externalpackages/m1qn3/install//libddot.a -L/home/natw/code/issm/trunk/externalpackages/petsc/install//lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps -lmetis -L/home/natw/code/issm/trunk/externalpackages/petsc/install// -lscalapack -L/home/natw/code/issm/trunk/externalpackages/mpich/install/lib -lpthread -lrt /home/natw/code/issm/trunk/externalpackages/mpich/install/lib/libmpich.so /home/natw/code/issm/trunk/externalpackages/mpich/install/lib/libmpl.so -Wl,-rpath -Wl,/home/natw/code/issm/trunk/lib -Wl,-rpath -Wl,/home/natw/code/issm/trunk/externalpackages/mpich/install/lib
/usr/bin/ld: /home/natw/code/issm/trunk/externalpackages/petsc/install/lib/libscalapack.a(PB_Cdtypeset.o): undefined reference to symbol 'dsyr2_'
/home/natw/code/issm/trunk/externalpackages/petsc/install/lib/libpetsc.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: ***  Error 1

mathieumorlighem

OK, so the default configure.sh is for macs. On Mac OS X, BLAS/LAPACK is provided by the OS and PETSc does not need to install it. In your case, since you are using Ubuntu, PETSc had to install BLAS and we need to tell ISSM to link against libfblas.lib as well. In your configure.sh add the following line:

--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \

run ./configure.sh again and recompile, you should be good to go.

Let us know if you have any other problem

Best

Mathieu

nwilson

Oh, right. Thanks, that got me a bit further.

Now I'm having trouble getting the Python bindings to build. I have a --with-python-dir line in the configuration script that points to the correct virtualenv, but the compilation is giving me

Making all in wrappers make: Entering directory `/home/natw/code/issm/trunk/src/wrappers' Making all in python make: Entering directory `/home/natw/code/issm/trunk/src/wrappers/python' CXX libISSMPython_la-WritePythonData.lo In file included from ./io/./pythonio.h, from ./io/WritePythonData.cpp: ./io/./../include/pythonincludes.h: fatal error: Python.h: No such file or directory #include <Python.h> ^ compilation terminated.

The output of `ls $HOME/venv-issm/include/python2.7` lists Python.h, so I'm not certain what's missing.

Thanks,

Nat