Re: [Libmesh-users] problem with ./configure

[Paul T. B. <ptb...@gm...>]

It looks like you haven't set PETSC_DIR and PETSC_ARCH. You need to set
these variables in your environment - these are how libMesh detects your
PETSc installation. Similarly for SLEPc (although I believe SLEPc is just
bundled with recent versions of PETSc, but don't quote me.)

On Wed, Aug 1, 2018 at 7:11 PM Harry Pearce <har...@gm...>
wrote:

> Paul,
> I fixed what I thought was causing a problem, but this didn't work. When I
> use ./configure --disable-metaphysicl --with-petsc --with-slepc libmesh
> becomes configured, but without petsc or slepc. I originally thought the
> problem was the .bashrc file, which defined the PATH for the petsc and
> slepc directories, but I fixed the bashrc file and this error still
> persists. A new config.log file is attached.
>
> Harrison Pearce
> SDSU Undergraduate in Chemical Physics
>
> On Wed, Aug 1, 2018 at 3:28 PM, Harry Pearce <har...@gm...>
> wrote:
>
>> Paul,
>> Here it is! There is another problem but I think I know what's causing it
>> so I will ask if I can't figure it out.
>>
>> Thanks again,
>> Harrison Pearce
>> SDSU undergraduate in Chemical Physics
>>
>> On Wed, Aug 1, 2018 at 3:10 PM, Paul T. Bauman <ptb...@gm...>
>> wrote:
>>
>>>
>>>
>>> On Wed, Aug 1, 2018 at 5:50 PM Harry Pearce <har...@gm...>
>>> wrote:
>>>
>>>> Paul,
>>>> Thanks! Your recommendation worked!
>>>>
>>>
>>> Great, glad you got it working. Let us know if you run into other issues.
>>>
>>>
>>>> My config.log file is attached just in case you still want to see it.
>>>>
>>>
>>> Thanks, but this is the one for your successful build. If you're
>>> willing, could you please pass along the for failed configure (when you
>>> didn't have --disable-metaphysicl)? Thanks!
>>>
>>>
>>>>
>>>> Thankfully,
>>>> Harrison Rojak Pearce
>>>> SDSU Undergraduate in Chemical Physics
>>>>
>>>> On Wed, Aug 1, 2018 at 1:34 PM, Paul T. Bauman <ptb...@gm...>
>>>> wrote:
>>>>
>>>>> Thanks for the report.
>>>>>
>>>>> If you don't need metaphysicl, probably the quickest thing you can do
>>>>> is pass `--disable-metaphysicl`
>>>>> to libmesh configure.
>>>>>
>>>>> What compiler are you using? I wonder if it's too old to build that
>>>>> boost module?
>>>>> Could you send along your config.log (can send to me directly, the
>>>>> mailing list will strip it).
>>>>> I'm curious to see what caused that failure.
>>>>>
>>>>> On Wed, Aug 1, 2018 at 4:17 PM Harry Pearce <har...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Hello fellow libmesh users!,
>>>>>>
>>>>>> I am trying to configure libmesh 1.3.0.
>>>>>> When I run ./configure I get the error:
>>>>>> checking for Boost headers version >= 1.47.0... yes
>>>>>> checking for Boost's header version... 1_55
>>>>>> checking for the toolset name used by Boost for mpicxx... configure:
>>>>>> WARNING: could not figure out which toolset name to use for mpicxx
>>>>>>
>>>>>> checking for the flags needed to use pthreads... conftest.cpp: In
>>>>>> function
>>>>>> 'int main()':
>>>>>> conftest.cpp:33:24: warning: null argument where non-null required
>>>>>> (argument 1) [-Wnonnull]
>>>>>>      pthread_attr_init(0); pthread_cleanup_push(0, 0);
>>>>>>                         ^
>>>>>> conftest.cpp:34:27: warning: null argument where non-null required
>>>>>> (argument 1) [-Wnonnull]
>>>>>>      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
>>>>>>                            ^
>>>>>> conftest.cpp:34:27: warning: null argument where non-null required
>>>>>> (argument 3) [-Wnonnull]
>>>>>> conftest.cpp:32:34: warning: 'th' is used uninitialized in this
>>>>>> function
>>>>>> [-Wuninitialized]
>>>>>>  pthread_t th; pthread_join(th, 0);
>>>>>>                                   ^
>>>>>> -pthread
>>>>>> configure: /vexcl/vexcl.hpp not found
>>>>>> configure: /include/vexcl/vexcl.hpp not found
>>>>>> checking whether we are using the Microsoft C++ compiler... no
>>>>>> checking CL/cl.h usability... no
>>>>>> checking CL/cl.h presence... no
>>>>>> checking for CL/cl.h... no
>>>>>> checking OpenCL/cl.h usability... no
>>>>>> checking OpenCL/cl.h presence... no
>>>>>> checking for OpenCL/cl.h... no
>>>>>> checking windows.h usability... no
>>>>>> checking windows.h presence... no
>>>>>> checking for windows.h... no
>>>>>> checking for OpenCL library... no
>>>>>> checking boost/system/error_code.hpp usability... yes
>>>>>> checking boost/system/error_code.hpp presence... yes
>>>>>> checking for boost/system/error_code.hpp... yes
>>>>>> checking for the Boost system library... yes
>>>>>> checking boost/chrono.hpp usability... yes
>>>>>> checking boost/chrono.hpp presence... yes
>>>>>> checking for boost/chrono.hpp... yes
>>>>>> checking for the Boost chrono library... (cached) yes
>>>>>> checking boost/date_time/posix_time/posix_time.hpp usability... no
>>>>>> checking boost/date_time/posix_time/posix_time.hpp presence... yes
>>>>>> configure: WARNING: boost/date_time/posix_time/posix_time.hpp:
>>>>>> present but
>>>>>> cannot be compiled
>>>>>> configure: WARNING: boost/date_time/posix_time/posix_time.hpp:
>>>>>>  check
>>>>>> for missing prerequisite headers?
>>>>>> configure: WARNING: boost/date_time/posix_time/posix_time.hpp: see the
>>>>>> Autoconf documentation
>>>>>> configure: WARNING: boost/date_time/posix_time/posix_time.hpp:
>>>>>>  section
>>>>>> "Present But Cannot Be Compiled"
>>>>>> configure: WARNING: boost/date_time/posix_time/posix_time.hpp:
>>>>>> proceeding
>>>>>> with the compiler's result
>>>>>> configure: WARNING:     ## --------------------------------------- ##
>>>>>> configure: WARNING:     ## Report this to roy...@ic... ##
>>>>>> configure: WARNING:     ## --------------------------------------- ##
>>>>>> checking for boost/date_time/posix_time/posix_time.hpp... no
>>>>>> configure: error: cannot find
>>>>>> boost/date_time/posix_time/posix_time.hpp
>>>>>> configure: error: ./configure failed for contrib/metaphysicl/0.2.0
>>>>>>
>>>>>>  I thought the problem may have had to do with the installation of
>>>>>> mpich
>>>>>> but I reinstalled it and the problem persists. I am wondering if the
>>>>>> problem is with libmesh, boost, or something else.
>>>>>>
>>>>>> I have read over some of the entries relating to this problem, and
>>>>>> they did
>>>>>> not help, although there are alot of entries so if someone has already
>>>>>> solved this problem and you can point me in the direction of their
>>>>>> post,
>>>>>> that also works.
>>>>>>
>>>>>> Thanks,
>>>>>> Harrison Rojak Pearce
>>>>>> SDSU undergraduate in Chemical Physics
>>>>>>
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>>>>>>
>>>>>
>>>>
>>
>