From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 20 2015 - 08:10:09 CDT
On Tue, Oct 20, 2015 at 8:39 AM, Puneet Singh <singh.punit1990_at_gmail.com>
wrote:
> Dear Sir,
> I am trying to build namd with fftw , i have multiple version of fftw at
> different locations . So to check which version of fftw my namd2 binary
> refers i did *ldd namd2* :
> linux-vdso.so.1 => (0x00007fff7f2ff000)
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003a1cc00000)
> libtcl8.5.so => /home/puneet/NAMD_BUILD/common_dependencies/lib/
> libtcl8.5.so (0x00002b1785241000)
> libm.so.6 => /lib64/libm.so.6 (0x0000003a1c800000)
> libmpicxx.so.12 => /opt/intel//impi/
> 5.0.1.035/intel64/lib/libmpicxx.so.12 (0x00002b17855c4000)
> libmpifort.so.12 => /opt/intel//impi/
> 5.0.1.035/intel64/lib/libmpifort.so.12 (0x00002b17857e4000)
> libmpi.so.12 => /opt/intel//impi/5.0.1.035/intel64/lib/libmpi.so.12
> (0x00002b1785a70000)
> librt.so.1 => /lib64/librt.so.1 (0x0000003a1d400000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003a1c400000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003a28400000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a27000000)
> libc.so.6 => /lib64/libc.so.6 (0x0000003a1c000000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003a1bc00000)
> libimf.so =>
> /opt/intel/composer_xe_2015.0.090/compiler/lib/intel64/libimf.so
> (0x00002b17861a3000)
> libsvml.so =>
> /opt/intel/composer_xe_2015.0.090/compiler/lib/intel64/libsvml.so
> (0x00002b178665e000)
> libirng.so =>
> /opt/intel/composer_xe_2015.0.090/compiler/lib/intel64/libirng.so
> (0x00002b17872ad000)
> libintlc.so.5 =>
> /opt/intel/composer_xe_2015.0.090/compiler/lib/intel64/libintlc.so.5
> (0x00002b17874b4000)
>
>
> fftw is not there in the dependency list & running this namd2 binary
> against apoa1 example with 500 steps (23 processes on 24 cores) finishes in
> 36 seconds without fftw routines!
>
the fftw library will only show up there, if fftw is linked in as a
dynamic library. if you link it from a static library, it won't generate a
dependency. the code of the library is directly copied into the executable.
axel.
>
> So i wish to know weather the namd2 binary needs fftw library ? I have
> doubts that i may not have configured properly ,The following command i am
> using to configure namd2:
>
> ./*config* mpi-linux-x86_64-MPI --charm-arch
> mpi-linux-x86_64-ifort-mpicxx --with-fftw --fftw-prefix
> $ROOT_DIR/common_dependencies --cxx icpc --cc icc --cc-opts --with-tcl
> --tcl-prefix $ROOT_DIR/common_dependencies
>
> I will be benchmarking against apoa1 example ,so, does solving against
> this input file needs fftw routines or can fftw routines improve namd
> performance (36 seconds) ?
>
> Eagerly Awaiting your reply,
>
> Thanks & Regards,
> Puneet Singh
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:09 CST