Hi Jason,
Thanks for your reply. I forwarded your e-mail to our ITS support who is
helping us to do the installation.For the error produced from trying sander.MPI
>This is evidence of either a broken OpenMPI installation or a borked
>environment.
>If I had to guess, I would say that your environment on this computer is
>a bit corrupted (possibly from too much Google-induced monkey patching
>to get stuff working -- I used to do that plenty). I am not sure if it is
related to some environment setup. I am able to run Amber 12 that is installed
on the same system without any trouble. However, Amber 12 was compiled using
Intel compiler not gcc. By the way, when we tried to compile Amber 14 with
Intel it did not work at all. That is why we decided to stick to your
instructions.
Thanks, Ibrahim
On Thu, Apr 2, 2015 02:59 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
On Thu, 2015-04-02 at 14:16 -0400, IBRAHIM M ABDELRADY wrote:
>> Dear Amber developer:We are trying to install Amber14 on our system but we
>are
>> having hard time doing that. I'm attaching the log file of the compiling
>to the
>> e-mail.Here is the information about the compiler & MPI we used and the
>> OS:Compiler: GCC 4.8.2, OpenMPI 1.8.1OS: Redhat 6.5We have followed the
>> instructions outlined in
>> http://jswails.wikidot.com/installing-amber14-and-ambertools14We started
>with
>> serial with gnu compilation and finished off with the
>> make test . Afterwards we tried the parallel with gnu compiler and then
>> we received errors. We experienced errors when testing amber14 with serial
>code
>> in particular the cpptraj executable had some errors. For some reason
>> cpptraj was looking at libstdc++.so.6 in intel version when the
>> compiler is set to gcc. It should be looking at
>> <gcc-home-dir>/lib64/libstdc++.so.6 These errors are outlined in
>> ambercompile.log file.
>
>I'll just point out here that cpptraj itself does not look for anything.
>foo.so is a shared library (.so == .Shared_Object). Unlike a static
>archive (foo.a), the symbols from a shared library are not compiled
>into
>the program you are building. One of the consequences here is that the
>library then needs to be loaded at runtime so the required symbols are
>defined. This task falls to the loader (ld)... we have no control
>over
>that.
>
>So what is really happening here is that the loader is loading libstdc
>++.so (which is a link to libstdc++.so.6) in the Intel compiler
>library
>directory. This happens because *something* in your environment or
>system configuration is telling ld to do that. For instance, check the
>value of the LD_LIBRARY_PATH and LIBRARY_PATH environment variables. I
>suspect that they contain your Intel library folders. I would suggest
>removing those.
>
>>
>> We noticed there was an error with ptraj executable when compiling in
>> parallel, so we tried to compile ptraj manually
>> $AMBERHOME/AmberTools/src/ptraj using make. The Makefile required
>> pnetcdf.h in $AMBERHOME/amber14/include which was not present so we
>> created the file and took the content from the web. We recompiled ptraj
>> again and it failed again. When we tried to test SANDER it worked fine;
>> however, SANDER.MPI did not work and gave errors.
>>
>> ../../../bin/cpptraj:
>>
>/usr/global/intel/composer_xe/2015.0.090/vtune_amplifier_xe_2015.1.0.367959/lib64/libstdc++.so.6:
>> version `GLIBCXX_3.4.15' not found (required by ../../../bin/cpptraj)
>
>This makes it seem like your Intel compilers (which are *very* new)
>don't work on this computer. They seem to require a GLIBC version that
>is newer than what RHEL 6.5 ships with. So as long as ld is trying to
>use Intel's libstdc++.so, cpptraj (or any other C++-based program, for
>that matter) will not work.
>
>> [snip]
>
>> Here is the error produced when trying to run sander.MPI:MD Simulation
>>
>> job started on lionxv96.hpc.rcc.psu.edu at Thu Apr 2 13:23:34 EDT 2015
>> sander.MPI: symbol lookup error: /usr/global/gcc-4.8.x/openmpi/1.8.1/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weig
>> hts_empty
>
>This is evidence of either a broken OpenMPI installation or a borked
>environment.
>
>If I had to guess, I would say that your environment on this computer is
>a bit corrupted (possibly from too much Google-induced monkey patching
>to get stuff working -- I used to do that plenty).
>
>Unfortunately, this kind of stuff can be a pain to debug remotely. I
>often have to take 5 to 10 minutes just inspecting the environment
>variables before I have an idea of what to try. Doing this process via
>email could take a long time; I would suggest trying to find a Linux
>expert locally and see if they can help you get this sorted.
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814)863 8703
Fax (814)865 7927
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Received on Thu Apr 02 2015 - 13:00:05 PDT
