Re: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program"

From: Frank Thommen (structures-it_at_embl-heidelberg.de)
Date: Mon Dec 02 2013 - 04:07:42 CST

Hi Norman,

we need this to run MPI jobs on the cluster. The MPI compilers - yes,
I'm aware that these are just wrappers - basically work. The MPI
installation as such is working fine. We have compiled several other
software packages using it and these applications are running fine on
the cluster.

PMPI is the only MPI implementation which is really integrated into the
LSF queueing system. We might use other MPI implementations if there is
no other way, but submitting clusterjobs will then become less
straightforward and sometimes quite cumbersome for the users. So the
idea is to have MPI software compiled for PMPI.

frank

On 02.12.13 09:05, Norman Geist wrote:
> Hi Frank,
>
> just for my interest, is there a special reason why you want a MPI instead
> of a simpler charm++ or precompiled build, this would save you from the
> trouble actually? If you really need a own MPI build of NAMD you should 1st
> make sure that your MPI installation is working at all. Please notice that
> "mpicc" and "mpic++" etc. are only wrappers that will call the original
> compiler used to build the mpi with the required libs and flags to compile a
> mpi using code. Therefore the compilers under this wrappers need to work,
> too. But it's not guaranteed from my understanding that every MPI will
> implement fine into charm++. Therefore I suggest trying another, more common
> MPI distribution, OpenMPI is known to work fine. From the log I can't see an
> obvious error regarding user input or usage, indicating some level of
> incompatibility of your MPI with charm++.
>
> Norman Geist.
>
>
>> -----Ursprngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Frank Thommen
>> Gesendet: Samstag, 30. November 2013 21:52
>> An: namd-l_at_ks.uiuc.edu
>> Betreff: namd-l: charm++ MPI build errors on LSF Cluster: "Can not
>> compile a MPI program"
>>
>> Hi,
>>
>> I'm currently having probleme building charm++ (6.4.0) with MPI for
>> namd
>> 2.9 on an CentOS 6.2 cluster running the LSF queueing system. As MPI
>> version we are using PMPI (Platform MPI), which has been delivered with
>> the cluster:
>>
>> # which mpiCC
>> /opt/platform_mpi/bin/mpiCC
>> # mpiCC --version
>> g++ (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
>> Copyright (C) 2010 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions. There is
>> NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>> #
>>
>> When running the charm++ build command (`env
>> MPICXX=/opt/platform_mpi/bin/mpiCC ./build charm++ mpi-linux-x86_64
>> --with-production`) the configure step reports the following checks as
>> failing:
>>
>> ===============================
>> checking "whether __int64 works"... "no"
>> checking "whether ucontext uses uc_regs"... "no"
>> checking "whether ucontext has pointer (v_regs) of vector type"... "no"
>> checking "whether GCC IA64 assembly works"... "no"
>> checking "whether PPC assembly works"... "no"
>> ===============================
>>
>>
>> And finally exits with an error:
>>
>> ===============================
>> [...]
>> Error: Can not compile a MPI program
>> *** Please find detailed output in charmconfig.out ***
>> gmake[1]: *** [conv-autoconfig.h] Error 1
>> gmake[1]: Leaving directory
>> `/g/software/linux/pack/namd-2.9/SRC/NAMD_2.9_Source/charm-6.4.0/mpi-
>> linux-x86_64/tmp'
>> gmake: *** [headers] Error 2
>> [...]
>> ===============================
>>
>> (The complete build output can be seen on http://pastebin.com/nBS62eWm)
>>
>>
>> In tmp/charmconfig.out above checks seem to relate to the following
>> errors:
>>
>> ===============================
>> test.cpp:2: error: '__int64' does not name a type
>> test.cpp:6: error: 'struct mcontext_t' has no member named 'uc_regs'
>> test.cpp:2: error: expected constructor, destructor, or type conversion
>> before '*' token
>> test.cpp:4: Error: invalid character '=' in operand 1
>> test.cpp:4: Error: no such instruction: `eieio'
>> ===============================
>>
>> (The complete content of tmp/charmconfig.out can be found on
>> http://pastebin.com/abuXNHKW)
>>
>>
>> Any ideas about what is going wrong and/or how this can be fixed, is
>> highly appreciated.
>>
>> Thank you very much in advance
>> Frank
>
>
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-- 
Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
structures-it_at_embl-heidelberg.de - +49 6221 387 8353

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