[petsc-users] Cross-compilation cluster

Sun Mar 17 22:23:39 CDT 2019

Apparently the problem is with openmpi 4.0 (or perhaps latest PETSc 3.10.4
not being compatible with it). I switched to openmpi 1.10.7 and PETSc 3.10,
which is what I was using on my workstation, and everything works fine.

====

Matt, I tried your suggestion. Apparently, Silo when compiled with mpi
wrappers (libsilo.a) does not produce link flags, as required by
AC_CHECK_LINKFLAGS(silo). When I compile it with serial compiler it does
not cause that check failure.

I noticed that configure help of openmpi has some options to add some extra
link flags. Perhaps it is supposed to circumvent situations like above.

On Thu, Mar 14, 2019 at 10:04 AM Amneet Bhalla <mail2amneet at gmail.com>
wrote:

> 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
>
>
>
> --
--Amneet
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