[petsc-users] Cross-compilation cluster

Thu Mar 14 09:05:16 CDT 2019

I need the serial built of Silo and HDF5 libraries. I am sure that the MPI
wrappers are coming from the serial compilers.

i.e, If I do

gcc —version and mpicc —version, I see the same GCC version.

On Thu, Mar 14, 2019 at 6:44 AM Matthew Knepley <knepley at gmail.com> wrote:

> It is very dangerous to use different compilers. I would make sure that
> all the compilers are the MPI compilers.
>
>   Thanks,
>
>     Matt
>
> On Thu, Mar 14, 2019 at 8:46 AM Amneet Bhalla <mail2amneet at gmail.com>
> wrote:
>
>> Ah, Ok. Do serial compilers look OK to you?
>>
>> Can lib-32 and lib-64 (say -lm) operate simulataneously during runtime,
>> or this is my imagination?
>>
>>
>>
>> On Thu, Mar 14, 2019 at 5:36 AM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> 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/>
>>>
>> --
>> --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
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