Petsc configure failure : --with-ml-lib

Take a look in /home/icw26/projects/FEniCS/src/petsc-3.2-p5/configure.log. It should tell you way it fails to work with ml.

Are you using Dorsal 1.0.0? I would recommend to use the development version instead.

Thanks for the reply Johannes,

I had looked at the petsc configure.log but couldn't understand why the problem occured.

I tried again with dorsal-1.0-beta2 as you suggested and Igot further. It crashed out when trying to download fiat and ufc from the web, because the web addresses were wrong. I replaced "trunk" with "1.0.x"for fiat and "2.0.x" for ufc, so that the addresses were valid and that helped.
It then had a problem compiling ufc, because the PYTHON_INCLUDE_DIR or PYTHON_LIBRARY flags are not set. Dorsal has downloaded its own python distribution, and I can't find it's include directory - "find . -name Python.h" in the FEniCS build directory gives nothing.

I tried setting the PYTHON_INCLUDE_DIR to one that I previously had on my computer "/home/icw26/include/python2.7", and the PYTHON_LIBRARY flag to a python library - "/home/icw26/lib/libpython2.7a", but this just made running dorsal_build for ufc give:
"
make[2]: Entering directory `/home/icw26/projects/FEniCS/src/ufc-2.0.3/dorsal_build_dir'
Linking CXX shared module _ufc.so
/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld: /home/icw26/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/home/icw26/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [_ufc.so] Error 1
"

This suggested that what I was doing was stupid. So, what should the PYTHON_INCLUDE_DIR or PYTHON_LIBRARY flags be for ufc?

Thanks again,

Iain

Sorry if I was being unclear, but with development version I meant the one from the Bazaar branch on Launchpad. You can fetch it by running:

  bzr branch lp:dorsal

(The 1.0-beta2 is older than 1.0.0.)

Hi Johannes,

I tried the development version and it fails in exactly the same place as dorsal1.0.0 , i.e. it fails in petsc, with the options --with-ml-lib and --with-ml-include .

Again, I couldn't understand why this was failing from the configure logs. I've put them on the internet, so if you have time to have a look at them then I would be grateful, because you're likely to see something that I will not.
http://www.srcf.ucam.org/~icw26/configure_logs/

Thanks,

Iain

The problem is almost at the bottom of configure.log, looking like this:

sh: mpicxx -o /tmp/petsc-3ehWJe/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O /tmp/petsc-3ehWJe/config.libraries/conftest.o -Wl,-rpath,/home/icw26/projects/FEniCS/lib -L/home/icw26/projects/FEniCS/lib -lml -llapack -lblas -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -L/usr/x86_64-suse-linux/lib -lmpichf90 -lgfortran -lm -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -lm -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -L/usr/x86_64-suse-linux/lib -ldl -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -lmpich -lopa -lpthread -lrt -lgcc_s -ldl
Executing: mpicxx -o /tmp/petsc-3ehWJe/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O /tmp/petsc-3ehWJe/config.libraries/conftest.o -Wl,-rpath,/home/icw26/projects/FEniCS/lib -L/home/icw26/projects/FEniCS/lib -lml -llapack -lblas -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -L/usr/x86_64-suse-linux/lib -lmpichf90 -lgfortran -lm -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -lm -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -L/home/icw26/projects/mpich2-install/lib -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -Wl,-rpath,/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -Wl,-rpath,/usr/x86_64-suse-linux/lib -L/usr/x86_64-suse-linux/lib -ldl -Wl,-rpath,/home/icw26/projects/mpich2-install/lib -lmpich -lopa -lpthread -lrt -lgcc_s -ldl
sh:
Possible ERROR while running linker: /usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_free_factor'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_transpose'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_analyze'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_start'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_analyze'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_free_sparse'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_finish'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_print_common'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_free_sparse'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_start'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `SuiteSparse_time'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_free_factor'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_transpose'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_finish'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_print_common'
collect2: ld returned 1 exit status
 output: ret = 256
error message = {/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_free_factor'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_transpose'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_analyze'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_start'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_analyze'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_free_sparse'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_finish'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_print_common'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_free_sparse'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_start'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `SuiteSparse_time'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_free_factor'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_transpose'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_l_finish'
/usr/lib64/libumfpack-5.6.1.so: undefined reference to `cholmod_print_common'
collect2: ld returned 1 exit status
}

One way to fix this will be to rebuild Trilinos and link it with the SuiteSparse libraries. Look at FEniCS/packages/trilinos.package (in Dorsal) where it tests for UMFPACK_DIR and modify it for your platform.

Thanks Johannes,

Modifying UMFPACK_DIR seems to have solved that problem. The installation continued until it reached ufc, where it failed in exactly the same manner as the second post above (which used dorsal-1.0-beta2). The ufc package does not know the value of the required flags PYTHON_INCLUDE_DIR and PYTHON_LIBRARY. The exact error message is included below.

I previously tried to set these myself (see above post) but this didn't help. Do you have any idea what I should set PYTHON_INCLUDE_DIR and PYTHON_LIBRARY to ?? In particular, I'm not sure what filenames that ufc is going to be looking for - i.e. does it want something called libpython? I only have one of them (libpython2.7.a) and it didn't like that last time because of an fPIC issue.

Any ideas? Thanks for taking the time to reply.

Iain

Building ufc-2.0.5
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
SWIG_MODULE_LOCATION /home/icw26/projects/FEniCS/src/ufc-2.0.5/dorsal_build_dir/_ufc.so
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PYTHON_INCLUDE_DIR (ADVANCED)
   used as include directory in directory /home/icw26/projects/FEniCS/src/ufc-2.0.5
PYTHON_LIBRARY (ADVANCED)
    linked by target "_ufc" in directory /home/icw26/projects/FEniCS/src/ufc-2.0.5

-- Configuring incomplete, errors occurred!

You should build the development versions of the FEniCS packages by setting STABLE_BUILD=false in dorsal.cfg. I'm not sure if that will fix the problem with UFC and Python, but let's try that first.

I've just re-run it with STABLE_BUILD=false. Exactly the same issue.

PYTHON_INCLUDE_DIR should be set to the directory which includes Python.h, while PYTHON_LIBRARY should point to the Python library (libpythonX.Y). These are normally detected automatically. Are you sure you have installed python-devel?

Yes, I have python-devel version 2.7-8.12.1, according to "zypper info python-devel", and it comes from the system packages.

I managed to solve the python problem above, however, by:
1) recompiling my python distribution with --enable-shared
2) setting PYTHON_INCLUDE_DIR=/home/icw26/include/python2.7, and the PYTHON_LIBRARY=/home/icw26/lib/libpython2.7.so in the ufc.package file.

Unfortunately there were then further complications:
1) A lot of the compile shared libraries in ${INSTALL_PATH}/lib had missing links. For example, libdolfin.so had no idea where any of the trilinos libraries that it wanted were set. I solved this by running "export LD_RUN_PATH= ${INSTALL_PATH}/lib" before running dorsal.sh . This helped with most of the missing links.
2) The dolfin module folder does not get copied to ${INSTALL_PATH}/lib/python2.7/site-packages , unlike dolfin_utils, which does get compiled to pyc files and then copied. Why is this ?

I tried to run the demo_navier-stokes.py file, and it could not import the dolfin module, because it did not know where it was. I copied the folder ${INSTALL_PATH}/src/dolfin/site-packages/dolfin to ${INSTALL_PATH}/lib/python2.7/site-packages . This resulted in the following error:

-----------
python demo_navier-stokes.py
Traceback (most recent call last):
  File "demo_navier-stokes.py", line 28, in <module>
    from dolfin import *
  File "/home/icw26/projects/FEniCS/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    import cpp
  File "/home/icw26/projects/FEniCS/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 40, in <module>
    exec("import %s" % module_name)
  File "<string>", line 1, in <module>
ImportError: No module named common
-----

'common' is a submodule in this dolfin module folder, but I think that cpp cannot find it because common is not a submodule in the cpp folder - i.e. the folder structure is dolfin->cpp and dolfin->common not dolfin->cpp->common. This suggested that just copying the dolfin folder across like I did is not a sensible way of doing things.

Do you have any idea why the dolfin module is not being installed properly? I have put the dorsal_configure.log and dorsal_build.log online in case that helps:
http://www.srcf.ucam.org/~icw26/configure_logs/

Thanks for the help,

Iain

Python support was not been enabled, as can be seen from the dorsal_configure.log:

-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) PYTHON
-- (**) SPHINX
-- (**) HDF5

Try to set PYTHON_INCLUDE_DIR and PYTHON_LIBRARY for DOLFIN like you did for UFC.

Thanks again Johannes, setting those python flags enabled the dolfin python module to install, just as you thought. Is it a problem that the other files listed are not found? Should I try and enable umfpack etc.?

The demo_navier-stokes file still crashed though. I believe that it is something to do with atlas. The output error was:

----------------------------------

python demo_navier-stokes.py
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
In instant.import_module_directly: Failed to import module 'dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd' from '/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd';
ImportError:/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd/_dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd.so: undefined symbol: ATL_zgemoveT;
Failed to import module found in cache. Modulename: 'dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd';
Path: '/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd';
ImportError:/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd/_dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd.so: undefined symbol: ATL_zgemoveT;
Traceback (most recent call last):
  File "demo_navier-stokes.py", line 52, in <module>
    p_in = Expression("sin(3.0*t)", t=0.0)
  File "/home/icw26/projects/FEniCS/lib64/python2.7/site-packages/dolfin/functions/expression.py", line 523, in __new__
    cpp_base, members = compile_expressions([cppcode])
  File "/home/icw26/projects/FEniCS/lib64/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 176, in compile_expressions
    code_snippets), classnames)
  File "/home/icw26/projects/FEniCS/lib64/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 114, in compile_expression_code
    compiled_module = compile_extension_module(code)
  File "/home/icw26/projects/FEniCS/lib64/python2.7/site-packages/dolfin/compilemodules/jit.py", line 66, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/home/icw26/projects/FEniCS/lib64/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 529, in compile_extension_module
    **instant_kwargs)
  File "/home/icw26/projects/FEniCS/lib/python2.7/site-packages/instant/build.py", line 494, in build_module
    module = import_and_cache_module(module_path, modulename, moduleids)
  File "/home/icw26/projects/FEniCS/lib/python2.7/site-packages/instant/cache.py", line 68, in import_and_cache_module
    instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).__name__, e))
  File "/home/icw26/projects/FEniCS/lib/python2.7/site-packages/instant/output.py", line 55, in instant_assert
    raise AssertionError(text)
AssertionError: Failed to import module found in cache. Modulename: 'dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd';
Path: '/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd';
ImportError:/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd/_dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd.so: undefined symbol: ATL_zgemoveT;

--------------------------------------------------------------

Again, any ideas that you have are greatly appreciated.

Iain

Interestingly, the cpp version of the navier-stokes demo compiles and runs ok, it is only the python version which does not.

Yes, it looks like it is not linking correctly with ATLAS. Take a look at FEniCS/packages/dolfin.package in Dorsal and try to modify for your ATLAS installation.

Thanks for the reply Johannes. Can you be any more specific about which flags I need to include? Or is there more information I can provide? I have just spend several more hours trying to solve this problem, but have run out of ideas. I have included a summary below of what I looked at, in case it is of any use.

1) examining the library that fails to load (/home/icw26/.instant/cache/dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd/_dolfin_compile_code_1d1ddc4d00703f8116bd2c7d25ec5bfd.so)

Running lddtree for this library shows that it finds all the .so files that it requires (recursively).

2) I checked the dolfin/dorsal_configure.sh file. It already contained flags that link to the atlas library:
declare -x BLAS_LIBRARIES="/usr/lib64/libblas.so;/usr/lib64/atlas/libcblas.a;/usr/lib64/atlas/libatlas.a"
(BLAS LIBRARIES is included in the CONFOPTS too)
declare -x LD_RUN_PATH="/home/icw26/projects/mpich2-install/lib:/home/icw26/projects/FEniCS/lib:/home/icw26/projects/FEniCS/lib64:/usr/lib64/atlas"
(This variable is also exported - but the libraries are static, so this shouldn't be a problem)

3) I tried manually adding flags to the CONFOPTS in the dorsal_configure file, in the same syntax as those for blas etc., but that did not seem to help.
-D LAPACK_LIBRARIES=/usr/lib64/liblapack.so -D ATLAS_INCLUDEDIR=/usr/include -D ATLAS_LIBRARYDIR=/usr/lib64/atlas -D ATLAS_LIBRARIES:FILEPATH="/usr/lib64/atlas/libcblas.a;/usr/lib64/atlas/libatlas.a"

4) I checked the static library /usr/lib64/libatlas.a using 'nm' for the symbol that is undefined (ATL_zgemoveT). It returned:
ATL_zgemoveT.o:
0000000000000000 T ATL_zgemoveT
                 U ATL_zgemoveT

5) I checked the library that fails to load (the one in .instant/cache) for undefined symbols. It has quite a few, some examples being:
.....U ATL_zgemaxnrm.....U PyArg_ParseTuple.....U _ZN6dolfin10ExpressionC2Ev....U cblas_cdotc_sub..... U exit@@GLIBC_2.2.5

6) dorsal_duild_dir/dolfin.pc has the atlas libs included in the Libs section: -L/usr/lib64/atlas -latlas -lcblas , so that looks fine.

Not knowing the exact process by which dorsal and dolfin are compiling/linking, I'm fairly out of my depth with this, so any suggestions that you have would be welcome.

Iain

Try switching the order of the libraries in dolfin.pc. That is, instead of

  -L/usr/lib64/atlas -latlas -lcblas

try this:

  -L/usr/lib64/atlas -lcblas -latlas

Thanks for the reply Johannes. I just tried that - having started again with your new dorsal version and trilinos 11 - but it did not change anything at all. Same ATL_zgemoveT symbol is undefined. I have even completely rebuilt and reinstalled atlas from scratch, that didn't help either.

Have you any other ideas what it could be? I have absolutely no idea, and am fairly close to giving up this end!

Iain

I'm afraid I'm running out of ideas.

One thing you could try is to let Dorsal build ATLAS.

I spent some time with Patrick Farrell yesterday, and he managed to get it up and running. Basically, FEniCS did not like the atlas static library. By providing it with a dynamic library equivalent, it was suddenly happy. I guess that this results in a minor loss of performance, but I'm just happy to have it up and running.

Thanks for all your help Johannes, I wouldn't have got this done without you. For others attempting to install on openSUSE 11.4, I have included a summary below of what helped me, although there are no guarantees that it will help!

Iain

#############################################
##############################################

INSTALLING ON OPENSUSE 11.4

This worked for me - it may not for you. I hope that it helps.

1) I used the development version of dorsal (at the time of writing), available with command: bzr branch lp:dorsal

2) Follow what dorsal.sh tells you to install. For SUSE 11.4, zypper does not have copies of several things that dorsal suggests. I had to also use:
wget http://www.opensuse-education.org/download/repo/1.0/11.1/suse/x86_64/umfpack-devel.rpm
rpm -Uvh umfpack-devel.rpm
wget http://www.opensuse-education.org/download/repo/1.0/11.1/suse/x86_64/libamd2_2_0.rpm
rpm -Uvh libamd2_2_0-2.2.0-9.8.x86_64.rpm
wget http://www.opensuse-education.org/download/repo/1.0/11.1/suse/x86_64/libumfpack5_2_0.rpm
rpm -Uvh libumfpack5_2_0-5.2.0-7.6.x86_64.rpm
zypper in hdf5
zypper in hdf5-devel
zypper in python-ply
zypper in python-devel

3) I had to recompile my python library with --enable-shared, so that I had a libpython.so file.

4) On openSUSE umfpack bits are default put in /usr/lib64/suitesparse and /usr/include/suitesparse . To allow for this, add UMFPACK_DIR=/usr to the end of dorsal.cfg
In trilinos.package change -D UMFPACK_LIBRARY_DIRS=${UMFPACK_DIR}/lib to end in lib64.

5) In trilinos.package, because my python library was not installed as root, I also had to add to the CONFOPTS: -D PYTHON_INCLUDE_DIRS:PATH=/home/icw26/include/python2.7 -D PYTHON_LIBRARIES=/home/icw26/lib/libpython2.7.so
This may not be necessary if your python is installed in /usr/lib or /usr/lib64 .

6) In dolfin.package, I had to give the directory to find armadillo, my python library again and umfpack again. I added to the CONFOPTS: -D UMFPACK_INCLUDE_DIRS=${UMFPACK_DIR}/include/suitesparse
 -D PYTHON_INCLUDE_DIR=/home/icw26/include/python2.7/ -D PYTHON_LIBRARY=/home/icw26/lib/libpython2.7.so
 -D ARMADILLO_DIR=${INSTALL_PATH}
 -D ARMADILLO_LIBRARYDIR=${INSTALL_PATH}/lib

7) I needed to use a shared atlas library, which isn't naturally provided by suse 11.4. Create a symlink to one that is there:
ln -s /usr/lib64/atlas/libsatlas.so.3 /usr/lib64/atlas/libsatlas.so

8) I needed to export LD_RUN_PATH in the shell before running ./dorsal.sh, because otherwise none of the libraries in ${INSTALL_PATH}/lib were linked. This looked like:
export LD_RUN_PATH=${INSTALL_PATH}lib:${INSTALL_PATH}/lib64:/usr/lib64/atlas