Hi,
Thanks for the link. I could go forward successfully as below, but finally
I still couldn't run sander.MPI, I mean I still can run amber in serial
(sander) not parallel.
Could you please let me know what I need to do?
cd /home/shirin/Software
tar xvfj AmberTools17.tar.bz2
tar xvfj Amber16.tar.bz2
export AMBERHOME=/home/myname/amber16
cd $AMBERHOME
./configure gnu
source /home/shirin/Software/amber16/amber.sh
make install
make test
Then Parallel:
download mpich-3.1.4.tar from
http://www.mpich.org/downloads/versions/
scp mpich-3.1.4.tar $AMBERHOME/AmberTools/src
cd $AMBERHOME/AmberTools/src
tar -xvf mpich-3.1.4.tar
./configure_mpich gnu
cd $AMBERHOME
./configure --help
./configure -mpi -cuda -openmp gnu
make install
export DO_PARALLEL="mpirun -np 2"
export DO_PARALLEL="mpirun -np 4"
export DO_PARALLEL="mpirun -np 8"
make test
cd $AMBERHOME/AmberTools/src
./configure_mpich gnu
Thanks,
Shirin
On Thu, Oct 5, 2017 at 11:57 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi
>
> http://archive.ambermd.org/201705/0382.html
>
> On Thu, Oct 5, 2017 at 6:24 PM Shirin Jamshidi <shirinjamshidi.gmail.com>
> wrote:
>
> > Could you please let me know what exactly I need to do?
> > I am not expert in this field and it is not a clear message to me.
> >
> > On Thu, Oct 5, 2017 at 11:20 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > > configure: error: could not find mpi library for --enable-mpi
> > >
> > > it's here.
> > >
> > > On Thu, Oct 5, 2017 at 5:41 PM, Shirin Jamshidi <
> > shirinjamshidi.gmail.com>
> > > wrote:
> > >
> > > > Dear AMBER experts,
> > > >
> > > > Following directions of Amber 16 manual
> > > >
> > > > I have successively passed amber 16 serial installation.
> > > > On the next step: installation of MPI
> > > > Amber 16 reports error:
> > > >
> > > > cd $AMBERHOME
> > > > ./configure -mpi -cuda -openmp gnu or
> > > > ./configure -mpi -cuda gnu or
> > > > ./configure -mpi gnu
> > > >
> > > > Configuring fftw-3.3 (may be time-consuming)...
> > > >
> > > > Error: FFTW configure returned 1
> > > > FFTW configure failed! Check the fftw3_config.log file
> > > > in the $AMBERHOME/AmberTools/src directory.
> > > > Configure failed due to the errors above!
> > > > Your advice how to fix the error highly appreciated.
> > > >
> > > >
> > > > Best,
> > > >
> > > > Shirin
> > > >
> > > >
> > > >
> > > >
> > > > fftw3_config.log file content :
> > > >
> > > > checking for a BSD-compatible install... /usr/bin/install -c
> > > > checking whether build environment is sane... yes
> > > > checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
> > > > checking for gawk... gawk
> > > > checking whether make sets $(MAKE)... yes
> > > > checking whether to enable maintainer-specific portions of
> Makefiles...
> > > no
> > > > checking build system type... x86_64-unknown-linux-gnu
> > > > checking host system type... x86_64-unknown-linux-gnu
> > > > checking for gcc... gcc
> > > > checking whether the C compiler works... yes
> > > > checking for C compiler default output file name... a.out
> > > > checking for suffix of executables...
> > > > checking whether we are cross compiling... no
> > > > checking for suffix of object files... o
> > > > checking whether we are using the GNU C compiler... yes
> > > > checking whether gcc accepts -g... yes
> > > > checking for gcc option to accept ISO C89... none needed
> > > > checking for style of include used by make... GNU
> > > > checking dependency style of gcc... gcc3
> > > > checking whether gcc and cc understand -c and -o together... yes
> > > > checking for C compiler vendor... gnu
> > > > checking for gcc option to accept ISO C99... -std=gnu99
> > > > checking for gcc -std=gnu99 option to accept ISO Standard C...
> (cached)
> > > > -std=gnu99
> > > > checking whether ln -s works... yes
> > > > checking whether make sets $(MAKE)... (cached) yes
> > > > checking for a sed that does not truncate output... /usr/bin/sed
> > > > checking for grep that handles long lines and -e... /usr/bin/grep
> > > > checking for egrep... /usr/bin/grep -E
> > > > checking for fgrep... /usr/bin/grep -F
> > > > checking for ld used by gcc -std=gnu99... /usr/bin/ld
> > > > checking if the linker (/usr/bin/ld) is GNU ld... yes
> > > > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> > > > checking the name lister (/usr/bin/nm -B) interface... BSD nm
> > > > checking the maximum length of command line arguments... 1572864
> > > > checking whether the shell understands some XSI constructs... yes
> > > > checking whether the shell understands "+="... yes
> > > > checking for /usr/bin/ld option to reload object files... -r
> > > > checking for objdump... objdump
> > > > checking how to recognize dependent libraries... pass_all
> > > > checking for ar... ar
> > > > checking for strip... strip
> > > > checking for ranlib... ranlib
> > > > checking command to parse /usr/bin/nm -B output from gcc -std=gnu99
> > > > object... ok
> > > > checking how to run the C preprocessor... gcc -std=gnu99 -E
> > > > checking for ANSI C header files... yes
> > > > checking for sys/types.h... yes
> > > > checking for sys/stat.h... yes
> > > > checking for stdlib.h... yes
> > > > checking for string.h... yes
> > > > checking for memory.h... yes
> > > > checking for strings.h... yes
> > > > checking for inttypes.h... yes
> > > > checking for stdint.h... yes
> > > > checking for unistd.h... yes
> > > > checking for dlfcn.h... yes
> > > > checking for objdir... .libs
> > > > checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
> > > > checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
> > > > checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
> > > > checking if gcc -std=gnu99 static flag -static works... no
> > > > checking if gcc -std=gnu99 supports -c -o file.o... yes
> > > > checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
> > > > checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m
> elf_x86_64)
> > > > supports shared libraries... yes
> > > > checking whether -lc should be explicitly linked in... no
> > > > checking dynamic linker characteristics... GNU/Linux ld.so
> > > > checking how to hardcode library paths into programs... immediate
> > > > checking whether stripping libraries is possible... yes
> > > > checking if libtool supports shared libraries... yes
> > > > checking whether to build shared libraries... yes
> > > > checking whether to build static libraries... yes
> > > > checking for ocamlbuild... no
> > > > checking for mpicc... no
> > > > checking for hcc... no
> > > > checking for mpcc... no
> > > > checking for mpcc_r... no
> > > > checking for mpxlc... no
> > > > checking for cmpicc... no
> > > > checking for MPI_Init... no
> > > > checking for MPI_Init in -lmpi... no
> > > > checking for MPI_Init in -lmpich... no
> > > > configure: error: could not find mpi library for --enable-mpi
> > > > _______________________________________________
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> > >
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Received on Fri Oct 06 2017 - 04:30:01 PDT
