[petsc-users] Cross-compilation cluster

Thu Mar 14 12:04:05 CDT 2019

Hmmn, ok. I will try it out.

On Thu, Mar 14, 2019 at 9:34 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Mar 14, 2019 at 10:05 AM Amneet Bhalla <mail2amneet at gmail.com>
> wrote:
>
>> 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.
>>
>
> That is in a perfect world. Unfortunately, flags for compilers can make
> incompatible libraries. Its no problem
> to give the MPI compilers to Silo and HDF5, even if you do not want to
> link the libraries.
>
>    Matt
>
>
>> 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
>>
>>
>>
>>
>
> --
> 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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