I tried the last suggestion from amber staff of re-untarring amber14 into
the folder again: the same make install crash results.
I notice that the call immediately before the final yacc crash (same crash
errors everytime I have tried this) is to the system libc.so.6 :
/ccs/home/adaa/AMBER/amber14/bin/yacc[0x404dfd]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x7f51769d5d1d]
/ccs/home/adaa/AMBER/amber14/bin/yacc[0x400ea9]
make[2]: *** [cifp.tab.c] Error 1
I wonder if there is a discrepancy between bison yacc and the system lib64
libraries. There is a lib64 directory in the AmberTools folder. I wonder if
I need to set a path to this to avoid the system version from being called?
On Sun, Jan 15, 2017 at 2:18 PM, Ada Sedova <ada.a.sedova.gmail.com> wrote:
> Here are the results of the checks you suggested:
>
> 1) mpicc -show shows the correct gcc (4.8.2) that I used for serial compile
>
> 2) serial config output has two outputs not found in mpi:
>
> Configuring XBLAS (may be time-consuming)...
>
> XBLAS configure succeeded.
>
> Configuring MTK++ (may be time-consuming)...
>
> MTK++-0.2.0 configure succeeded.
>
> 3) mpi config output has the expected difference:
>
> testing [C++ / fortran] cross-compile with MPI libs
>
> However, there is no "OK" or other success message after this call, simply:
>
> "The configuration file, config.h, was successfully created."
>
> immediately after the above call.
>
>
> Otherwise, the two outputs are identical.
>
>
> I am going to try to keep building amber14, but the idea of switching to
> 16 is a possibility for the future.
>
> On Sun, Jan 15, 2017 at 1:42 PM, David Case <david.case.rutgers.edu>
> wrote:
>
>> On Sat, Jan 14, 2017, Ada Sedova wrote:
>> >
>> > My colleagues at the NCCS Scientific Computing group also were wondering
>> > why you would HAVE to build in serial first (it is not a common
>> procedure).
>>
>> The reasoning is this: Amber users potentially need all the programs
>> in the suite, but only a few are configured for parallel operation.
>> Furthermore, the parallel programs need to be compiled with mpicc/mpif90,
>> whereas the other codes don't need this. So it makes sense to ask
>> parallel users to compile both serial and parallel versions (the latter
>> only creates a few executables.)
>>
>> But since there are some users who need only parallel programs for a
>> particular computer (cluster), we will try to allow for parallel-only
>> builds
>> in the next release of AmberTools.
>>
>> > Also, it is strange that after advising me to do this, they are also
>> > telling me that there is a common problem with residual files from the
>> > serial build interfering with the parallel build, and I should use <make
>> > distclean>; furthermore there is no rule for distclean, only for clean,
>> in
>> > the top Makefile. Very confusing.
>>
>> This is more or less inevitable in a mailing list. The Amber16
>> distribution's
>> Makefile has a "distclean" target, whereas that from Amber14 apparently
>> does
>> not.
>>
>> And no, these problems are not "common". Since it is often hard to debug
>> problems that do arise remotely, a reasonable suggestion is to try to make
>> sure that we understand the environment at the remote site, hence the
>> suggestion to try to start from a clean environment.
>>
>> >
>> > While I have your attention, I was wonder what it would take to get an
>> > upgrade of our site license to amber16/AmberTools16.
>>
>> Please visit http://ambermd.org/#obtain. (Note: be sure to check your
>> mpicc
>> command as I suggested earlier, or you may find the same problem with
>> Amber16:
>> I'm not sure that the root cause of your problem has really been
>> identified.
>> Also note that you can see if things work just with AmberTools16, since
>> the
>> problem you report was with the AmberTools parallel build.)
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Jan 15 2017 - 12:00:02 PST
