[mpich-discuss] mpich-3.2 34
Kenneth Raffenetti
raffenet at mcs.anl.gov
Wed Jan 6 11:10:42 CST 2016
You may need to add an explicit -lc flag to your LDFLAGS. Or if that
doesn't work, you could try to LD_PRELOAD it.
On 01/05/2016 01:40 PM, Professor W P Jones wrote:
> Hi Jeff
>
> Yes /usr/lib64/libc.so does exist on my machine! But how do I configure
> mpich to use this libc?
>
> Thanks
> Bill
>
> Professor W P Jones
> Department of Mechanical Engineering
> Imperial College London
> Exhibition Road
> London SW7 2AZ
> Tel: +44 (0)20 7594 7037/7033
> Mobile +44 (0)776 495 9702
> Fax: +44 (0)20 7594 5702
> E-mail:w.jones at imperial.ac.uk
> web site:http://www.imperial.ac.uk/me
>
> On 05/01/16 21:07, Jeff Hammond wrote:
>> According to
>> http://www.pgroup.com/userforum/viewtopic.php?t=539&view=previous&sid=50478c97090822511008dc30128ee908
>> and
>> http://www.linuxquestions.org/questions/linux-software-2/gcc-linker-error-hidden-symbol-%60stat'-in-usr-lib-libc_nonshared-a-stat-os-755962/
>> <http://www.linuxquestions.org/questions/linux-software-2/gcc-linker-error-hidden-symbol-%60stat%27-in-usr-lib-libc_nonshared-a-stat-os-755962/>,
>> it looks like a glibc issue.
>>
>> It might help to verify that the libc you are getting in this case is
>> the right one and it works. You are getting one that appears designed
>> for static linkage. Is there no /usr/lib64/libc.so on your machine?
>>
>> Jeff
>>
>> On Tue, Jan 5, 2016 at 11:04 AM, Professor W P Jones
>> <<mailto:w.jones at imperial.ac.uk>w.jones at imperial.ac.uk> wrote:
>>
>> Hi Ken
>>
>> I can send you the Makefile and output but the code has run
>> successfully using various other flavours of mpi and compilers -
>> mpich2, openmpi, intel mpi, gfortran and ifort etc. The example
>> program pi3f90.f90 produces a similar error:
>>
>> wpj at kelvin:f90 20 mpif90 pi3f90.f90
>> Encountered 0 errors, 0 warnings in file pi3f90.f90.
>> /usr/bin/ld: a.out: hidden symbol `lstat64' in
>> /usr/lib64/libc_nonshared.a(lstat64.oS) is referenced by DSO
>> /usr/bin/ld: final link failed: Nonrepresentable section on output
>>
>> Regards
>> Bill
>>
>> Professor W P Jones
>> Department of Mechanical Engineering
>> Imperial College London
>> Exhibition Road
>> London SW7 2AZ
>> Tel: +44 (0)20 7594 7037/7033
>> Mobile +44 (0)776 495 9702
>> Fax: +44 (0)20 7594 5702
>> E-mail: w.jones at imperial.ac.uk <mailto:w.jones at imperial.ac.uk>
>> web site: http://www.imperial.ac.uk/me
>>
>> On 05/01/16 18:08, Kenneth Raffenetti wrote:
>>
>> Hi,
>>
>> Do you have a make log from the application you are trying to
>> build that you can share?
>>
>> Separately, did the example cpi application build successfully
>> at the end of the MPICH build?
>>
>> Ken
>>
>> On 01/05/2016 02:44 AM, Professor W P Jones wrote:
>>
>> Hi
>>
>> I have successfully compiled and installed the version
>> suggested.
>> However when I attempt to to use make to compile and link
>> it fails on
>> the link step with the message:
>>
>> /usr/bin/ld: boffin: hidden symbol `lstat64' in
>> /usr/lib64/libc_nonshared.a(lstat64.oS) is referenced by DSO
>> /usr/bin/ld: final link failed: Nonrepresentable section
>> on output
>> make: [boffin] Error 1 (ignored)
>> mv: cannot stat `./x86_64/boffin': No such file or directory
>> make: *** [boffin] Error 1
>>
>> The log files generated in the compiled and install are
>> attached and
>> the output from mpiexec -info is:
>>
>> HYDRA build details:
>> Version: 3.2
>> Release Date: Mon Jan 4
>> 00:00:40 CST 2016
>> CC: icc
>> CXX: icpc
>> F77: lf95
>> F90: lf95
>> Configure options: '--disable-option-checking'
>> '--prefix=/opt/mpich' '--enable-fortran=all' 'FC=lf95'
>> 'F77=lf95'
>> '--cache-file=/dev/null' '--srcdir=.' 'CC=icc' 'CFLAGS=
>> -O2' 'LDFLAGS='
>> 'LIBS=-lpthread ' 'CPPFLAGS=
>> -I/usr/local/src/mpich-master-v3.2-42-g67631a5c0e9e/src/mpl/include
>> -I/usr/local/src/mpich-master-v3.2-42-g67631a5c0e9e/src/mpl/include
>> -I/usr/local/src/mpich-master-v3.2-42-g67631a5c0e9e/src/openpa/src
>> -I/usr/local/src/mpich-master-v3.2-42-g67631a5c0e9e/src/openpa/src
>> -D_REENTRANT
>> -I/usr/local/src/mpich-master-v3.2-42-g67631a5c0e9e/src/mpi/romio/include'
>>
>> 'MPLLIBNAME=mpl'
>> Process Manager: pmi
>> Launchers available: ssh rsh fork
>> slurm ll lsf
>> sge manual persist
>> Topology libraries available: hwloc
>> Resource management kernels available: user slurm
>> ll lsf sge pbs
>> cobalt
>> Checkpointing libraries available:
>> Demux engines available: poll select
>>
>> Regards
>> Bill
>>
>> Professor W P Jones
>> Department of Mechanical Engineering
>> Imperial College London
>> Exhibition Road
>> London SW7 2AZ
>> Tel: +44 (0)20 7594 7037/7033
>> Mobile +44 (0)776 495 9702
>> Fax: +44 (0)20 7594 5702
>> E-mail: w.jones at imperial.ac.uk <mailto:w.jones at imperial.ac.uk>
>> web site: http://www.imperial.ac.uk/me
>>
>> On 04/01/16 15:55, Kenneth Raffenetti wrote:
>>
>> Can you try the latest nightly tarball on the MPICH
>> website? I
>> committed a patch last night that I believe addresses
>> the issue. I
>> don't have a system with the lf95 compiler to test, so
>> I just went
>> from the documentation.
>>
>> Ken
>>
>> On 12/27/2015 07:49 PM, Professor W P Jones wrote:
>>
>> Hi Pavan
>>
>> Here are all the existing log files.
>>
>> Regards
>> Bill
>>
>> Professor W P Jones
>> Department of Mechanical Engineering
>> Imperial College London
>> Exhibition Road
>> London SW7 2AZ
>> Tel: +44 (0)20 7594 7037/7033
>> Mobile +44 (0)776 495 9702
>> Fax: +44 (0)20 7594 5702
>> E-mail: w.jones at imperial.ac.uk
>> <mailto:w.jones at imperial.ac.uk>
>> web site: http://www.imperial.ac.uk/me
>>
>> On 28/12/15 00:40, Balaji, Pavan wrote:
>>
>> Could you send us the log files listed in the
>> README?
>>
>> http://git.mpich.org/mpich.git/blob/HEAD:/README.vin#l235
>>
>> -- Pavan
>>
>> On Dec 27, 2015, at 5:34 AM, Professor W P
>> Jones
>> <w.jones at imperial.ac.uk
>> <mailto:w.jones at imperial.ac.uk>> wrote:
>>
>> Hi
>>
>> I am trying to build MPICH-3.2 34 using
>> Lahey/Fujitsu Linux64
>> Fortran Express Release L8.10b and I
>> obtain the following error:
>>
>> checking for Fortran 90 module output
>> directory flag...
>> configure: error: FCMODOUTFLAG could not
>> be determined but is
>> critical for the current Fortran build system
>>
>> Please can you advise how this can be fixed?
>>
>> Many thanks
>> Bill Jones
>>
>> --
>> Professor W P Jones
>> Department of Mechanical Engineering
>> Imperial College London
>> Exhibition Road
>> London SW7 2AZ
>> Tel: +44 (0)20 7594 7037/7033
>> Mobile +44 (0)776 495 9702
>> Fax: +44 (0)20 7594 5702
>> E-mail: w.jones at imperial.ac.uk
>> <mailto:w.jones at imperial.ac.uk>
>> web site: http://www.imperial.ac.uk/me
>>
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>> --
>> Jeff Hammond
>> jeff.science at gmail.com <mailto:jeff.science at gmail.com>
>> http://jeffhammond.github.io/
>>
>>
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