Of course, I can use GNU compilers, however, I won't be able to use MKL.
Seems like now MKL linking with GNU compilers is not supported and
disabled in configure2 file.
18.09.2019 23:16, Scott Brozell пишет:
> Hi,
>
> I recommend trying new compilers.
> Generally, recent GNU compilers produce executables that
> perform as good as Intel compilers. Of course, details
> can matter, so if you have benchmarks for Amber18 using your system
> that compare compiler performance, we'd be interested in the results.
>
> I made a brief attempt to build sander with intel/15.0.3 and mkl;
> there was a compiler error because intel 15 mkl is so old it does not
> have fftw3.f03
>
> scott
>
> ps snippets below show the failure and compare mkl 15 vs 16 :
>
> ===
> ...
> [SANDER] FC rmsgrd.F90
> [SANDER] FC ../lib/AmberNetcdf.F90
> cd ../rism && \
> if [ -n "-DRISMSANDER" ]; then \
> make amber_rism_interface.SANDER.o; \
> else \
> test -e amber_rism_interface.SANDER.o || touch amber_rism_interface.SANDER.o; \
> fi
> make[3]: Entering directory `/tmp/amber/AmberTools/src/rism'
> [RISM] FC rism_report_c.F90
> [RISM] FC fftw3.F90
> fftw3.F90(36): error #5102: Cannot open include file 'fftw3.f03'
> include 'fftw3.f03'
> ----------^
> compilation aborted for fftw3.F90 (code 1)
> make[3]: *** [fftw3.o] Error 1
> make[3]: Leaving directory `/tmp/amber/AmberTools/src/rism'
> make[2]: *** [../rism/amber_rism_interface.SANDER.o] Error 2
> make[2]: Leaving directory `/tmp/amber/AmberTools/src/sander'
> ===
>
> ===
> ll /usr/local/intel/composer_xe_2015.3.187/mkl/include/fftw
> total 124
> 4 -rw-r--r-- 1 root root 2788 Apr 10 2015 fftw3.f
> 28 -rw-r--r-- 1 root root 22978 Apr 10 2015 fftw3.h
> 4 -rw-r--r-- 1 root root 1731 Apr 10 2015 fftw3_mkl.f
> 28 -rw-r--r-- 1 root root 22263 Apr 10 2015 fftw3_mkl_f77.h
> 4 -rw-r--r-- 1 root root 2623 Apr 10 2015 fftw3_mkl.h
> 12 -rw-r--r-- 1 root root 9346 Apr 10 2015 fftw3-mpi.h
> 4 -rw-r--r-- 1 root root 2835 Apr 10 2015 fftw3-mpi_mkl.h
> 4 -rw-r--r-- 1 root root 1436 Apr 10 2015 fftw_f77.i
> 12 -rw-r--r-- 1 root root 11897 Apr 10 2015 fftw.h
> 8 -rw-r--r-- 1 root root 6467 Apr 10 2015 fftw_mpi.h
> 4 -rw-r--r-- 1 root root 1201 Apr 10 2015 fftw_threads.h
> 4 -rw-r--r-- 1 root root 3285 Apr 10 2015 rfftw.h
> 4 -rw-r--r-- 1 root root 2966 Apr 10 2015 rfftw_mpi.h
> 4 -rw-r--r-- 1 root root 1585 Apr 10 2015 rfftw_threads.h
> ===
>
> ===
> lll /usr/local/intel/compilers_and_libraries_2016/linux/mkl/include/fftw/
> total 220
> 4 -rw-r--r-- 1 root root 3833 Jan 18 2016 fftw3.f
> 60 -rw-r--r-- 1 root root 55115 Mar 17 2016 fftw3.f03
> 20 -rw-r--r-- 1 root root 17896 Mar 17 2016 fftw3.h
> 4 -rw-r--r-- 1 root root 1661 Jan 18 2016 fftw3_mkl.f
> 28 -rw-r--r-- 1 root root 22172 Jan 18 2016 fftw3_mkl_f77.h
> 4 -rw-r--r-- 1 root root 2589 Jan 18 2016 fftw3_mkl.h
> 44 -rw-r--r-- 1 root root 38059 Mar 17 2016 fftw3-mpi.f03
> 12 -rw-r--r-- 1 root root 9621 Mar 17 2016 fftw3-mpi.h
> 4 -rw-r--r-- 1 root root 2468 Jan 18 2016 fftw3-mpi_mkl.h
> 4 -rw-r--r-- 1 root root 1436 Oct 22 2014 fftw_f77.i
> 12 -rw-r--r-- 1 root root 11897 Oct 22 2014 fftw.h
> 8 -rw-r--r-- 1 root root 6462 Mar 17 2016 fftw_mpi.h
> 4 -rw-r--r-- 1 root root 1201 Oct 22 2014 fftw_threads.h
> 4 -rw-r--r-- 1 root root 3280 Mar 17 2016 rfftw.h
> 4 -rw-r--r-- 1 root root 2966 Jan 22 2016 rfftw_mpi.h
> 4 -rw-r--r-- 1 root root 1585 Oct 22 2014 rfftw_threads.h
> ===
>
> On Mon, Sep 16, 2019 at 03:32:25PM +0300, viktor drobot wrote:
>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fftp.desolve.ru%2Fftp%2Fviktor%2Ftest_case.tar.gz&data=02%7C01%7Csbrozell%40iqb.rutgers.edu%7Cfa7911f483654b16639d08d73aa1f7ac%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637042339640121956&sdata=yDfFVx%2F25DaQKki6IVVeKE0lElpKQ30P3S6PLQv6Chk%3D&reserved=0
>>
>> Here are my test case with 4 variants for dynamics - plain dynamics,
>> metadynamics, qm/mm dynamics and qm/mm metadynamics. Running on our
>> Lomonosov-2 cluster with GCC-4.8.5/CUDA-8.0 works just fine for all
>> modules (sander and sander.MPI [all types of dynamics]; pmemd,
>> pmemd.MPI, pmemd.cuda, pmemd.cuda.MPI [dynamics without QM/MM]).
>> However, using Intel-15.0.3 compilers with MKL 2015.3.187-lp64 leads to
>> fails with sander.MPI module (silent segfault) and nice working with
>> other modules.
>>
>> 16.09.2019 15:21, David A Case ??????????:
>>> On Sun, Sep 15, 2019, viktor drobot wrote:
>>>
>>>> It's very pity because I can't use QM/MM with high-performance Intel
>>>> compilers and MKL library which gives some boost. What I can do to find
>>>> out the cause of this bug? Thank you!
>>> Can you create a small test case, and post the files involved? We would
>>> need to be able to reproduce the problem before trying to debug it.
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Received on Wed Sep 18 2019 - 15:00:02 PDT
