[petsc-users] Cross-compilation cluster

Thu Mar 14 07:36:07 CDT 2019

On Thu, Mar 14, 2019 at 8:28 AM Amneet Bhalla <mail2amneet at gmail.com> wrote:

> Matt -- SAMRAI, PETSc, and libMesh configure logs are attached with this
> email. Also including some other log files in case they are useful.
>

Okay, PETSc is not sticking in a /usr/lib (or /usr/lib64). However, I can
see that you mpif90 (and perhaps other of the wrappers) are
reporting both /usr/lib64 AND /usr/lib flags, and I am guessing that is
where the other configures are picking it up.

  Thanks,

    Matt

> Thanks,
> --Amneet
>
> On Thu, Mar 14, 2019 at 4:21 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> In order to see why each flag was included, we need to see configure.log.
>>
>>   Thanks,
>>
>>      Matt
>>
>> On Thu, Mar 14, 2019 at 2:40 AM Amneet Bhalla via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Hi Folks,
>>>
>>> I am on a cluster that has -L/lib dir with 32-bit libraries and -L/lib64
>>> with 64-bit libraries. During compilation of some of libraries required for
>>> my code (such as SAMRAI and libMesh) both paths
>>> get picked  -L/lib and -L/lib64.
>>>
>>> I am seeing some sporadic behavior in runtime when at some timesteps
>>> PETSc does not converge. The same code with the same number of processors
>>> run just fine on my workstation that has just 64-bit version of libraries.
>>>
>>> Even during the final linking stage of the executable, the linker gives
>>> warnings like
>>>
>>> ld: skipping incompatible //lib/libm.so when searching for -lm
>>>
>>> ld: skipping incompatible /lib/libm.so when searching for -lm
>>>
>>> ld: skipping incompatible /lib/libm.so when searching for -lm
>>>
>>> ld: skipping incompatible //lib/libpthread.so when searching for
>>> -lpthread
>>>
>>> ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
>>>
>>> ld: skipping incompatible /lib/libpthread.so when searching for -lpthread
>>>
>>> ld: skipping incompatible //lib/libdl.so when searching for -ldl
>>>
>>> ld: skipping incompatible //lib/libc.so when searching for -lc
>>>
>>> ld: skipping incompatible /lib/libc.so when searching for -lc
>>>
>>> ld: skipping incompatible /lib/libc.so when searching for -lc
>>> but the executable runs.
>>>
>>>
>>> This is during config of SAMRAI when it picks both -L/lib and -L/lib64:
>>>
>>> checking whether we are using the GNU Fortran 77 compiler... no
>>>
>>> checking whether ifort accepts -g... yes
>>>
>>> checking how to get verbose linking output from ifort... -v
>>>
>>> checking for Fortran 77 libraries of ifort...
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.4
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/ -L/lib/../lib64
>>> -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.4/
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64/
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64/
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../ -L/lib64 -L/lib/
>>> -L/usr/lib64 -L/usr/lib -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc
>>> -lpthread -lgcc -lgcc_s -lirc_s -ldl
>>>
>>> libMesh is also picking that path
>>>
>>> libmesh_optional_LIBS............ : -lhdf5 -lhdf5_cpp -lz
>>> -L/home/asbhalla/softwares/PETSc-BitBucket/PETSc/linux-opt/lib
>>> -Wl,-rpath,/home/asbhalla/softwares/PETSc-BitBucket/PETSc/linux-opt/lib
>>> -Wl,-rpath,/opt/intel/mkl/lib/intel64 -L/opt/intel/mkl/lib/intel64
>>> -Wl,-rpath,/opt/mellanox/hcoll/lib -L/opt/mellanox/hcoll/lib
>>> -Wl,-rpath,/opt/mellanox/mxm/lib -L/opt/mellanox/mxm/lib
>>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.4
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.4
>>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64
>>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64
>>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64
>>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin
>>> -L/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin
>>> -lpetsc -lHYPRE -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
>>> -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lifport
>>> -lifcoremt_pic -limf -lsvml -lm -lipgo -lirc -lpthread -lgcc_s -lirc_s
>>> -lstdc++ -ldl -L/lib -Wl,-rpath,/lib
>>> -Wl,-rpath,/usr/local/mpi/intel/openmpi-4.0.0/lib64
>>> -L/usr/local/mpi/intel/openmpi-4.0.0/lib64
>>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>>>
>>> Perhaps PETSc also picks up both versions (and there is a way to query
>>> it from PETSc?), but I can't confirm this. Is there a way to instruct make
>>> to select only -L/lib64? I want to rule out that 32-bit dynamic library is
>>> not a culprit for the random non-convergence of PETSc solvers and the
>>> eventual crash of the simulations. I have tried both gcc-7.3.0 and intel-18
>>> compilers -- but the same thing is happening.
>>>
>>>
>>> --
>>> --Amneet
>>>
>>>
>>>
>>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
>
> --
> --Amneet
>
>
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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