I can say that building Amber14 on RHEL5 with Intel Composer XE compilers version 15.0.2 (newer than this guy’s — the latest available; he’s got 15.0.0), everything works fine. I don’t know what that vtune_amplififer_xe thing is, but it’s not part of the main compiler suite.
> On Apr 2, 2015, at 2:59 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
>
>
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Received on Thu Apr 02 2015 - 12:30:03 PDT
