Operating system : Fedora 22 (64 bit) system.
compiler : gnu - 5.3.1
These are the steps i have used to install ambertools
tar xvfj AmberTools15.tar.bz2
export AMBERHOME=/home/kronos/newamber/amber14
sudo apt-get install csh flex gfortran g++ xorg-dev zlib1g-dev libbz2-dev
patch python-tk python-matplotlib
sudo yum install gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel
bzip2-devel libXt-devel libXext-devel libXdmcp-devel python-devel tkinter
numpy scipy python-matplotlib openmpi openmpi-devel perl
perl-ExtUtils-MakeMaker patch bison
cd $AMBERHOME
./configure -mpi gnu
output from configure:
"Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
update.1 (modifies MMPBSA.py, ParmEd, cpptraj)
update.2 (modifies AmberTools, CUDA)
update.3 (modifies nab, sff)
update.4 (modifies Leap, Lipid14, force, field)
update.5 (modifies ParmEd)
update.6 (modifies pmemd.cuda)
There are patches available. Do you want to apply them now? [y/N]
(Recommended Y)
n
NOT updating your tree and continuing anyway.
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 5.3.1
The Fortran version is 5.3.1
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Compiling the NetCDF C interface (may be time-consuming)...
Configuring NetCDF Fortran interface (may be time-consuming)...
Compiling the NetCDF Fortran interface (may be time-consuming)...
NetCDF build succeeded.
Checking for zlib:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -lz -o
testp testp.c
OK
Checking for libbz2:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-lbz2 -o testp testp.c
OK
Configuring fftw-3.3 (may be time-consuming)...
Error: FFTW configure returned 1
FFTW configure failed! Check the fftw3_config.log file
in the /home/kronos/sim/amber14/AmberTools/src directory.
Configure failed due to the errors above!"
I checked "fftw3_config.log" file. It is showing (last few lines)
"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"
my system has mpi/openmpi-x86_64 installed in it.
On Mon, Apr 4, 2016 at 4:27 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> Yes, you would have to use sander.MPI if you plan to run in parallel and
> you would configure the build in the way you say.
>
> If there is a problem in the configuration step you would need to provide
> all of the output from configure, tell us what the exact command line was
> and also what operating system version and compiler version you are using.
> Only then will it be possible for the developers to find out what was going
> wrong.
>
> ________________________________________
> From: Sreemol G [sreemolinfo.gmail.com]
> Sent: 04 April 2016 11:39
> To: AMBER Mailing List
> Subject: Re: [AMBER] General question
>
> I'm not using sander.MPI. To use this do we need to configure using -mpi
> while installing amber??? I have tried "configure -mpi gnu" but I got
> error "fftw-3.3 configuration failed"
> On 04-Apr-2016 3:47 pm, <hannes.loeffler.stfc.ac.uk> wrote:
>
> > There is no OpenMP version of sander. It may be a good idea to read
> > through the first chapter of the manual to understand the build
> procedure.
> >
> > If you want to run sander in parallel you have to make the MPI version
> and
> > run it according to the MPI library you are using, typicall through a
> > program called "mpirun" (but may also be a very different name, see the
> > respective documentation).
> >
> > I think MDOUT always tells you how many nodes you use when you use
> > sander.MPI. Are you sure that you were using the right executable and
> are
> > calling it correclty?
> >
> > ________________________________________
> > From: Sreemol G [sreemolinfo.gmail.com]
> > Sent: 04 April 2016 10:57
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] General question
> >
> > I have uninstalled that program and reinstalled again. In the second
> time i
> > used -openmp flag instead of -mpi. After this I was not able to run make
> > test. It is giving this error
> > "[root.Kronos amber14]# make test
> > make: *** No rule to make target 'test.openmp', needed by 'test'. Stop."
> >
> >
> > On Mon, Apr 4, 2016 at 12:38 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> >
> > > Have you compiled and are you running sander.MPI?
> > > ________________________________________
> > > From: Sreemol G [sreemolinfo.gmail.com]
> > > Sent: 04 April 2016 07:47
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] General question
> > >
> > > I'm using sander for running simulation.. I already checked mdout file
> > but
> > > I didn't find line "Running AMBER/MPI version on 4 nodes" in mdout
> > file.
> > > If I want to run the program in parallel what should I do???
> > > Both sander and pmemd report what version is running and how many
> > "nodes"
> > > have been used. Look into the MDOUT file.
> > >
> > > ________________________________________
> > > From: Sreemol G [sreemolinfo.gmail.com]
> > > Sent: 04 April 2016 07:04
> > > To: AMBER Mailing List
> > > Subject: [AMBER] General question
> > >
> > > Hi all,
> > >
> > > Can anyone tell me the command to check whether amber
> simulation
> > > is running in parallely in all core (N=4). For running 500ps simulation
> > it
> > > took almost 19 hrs of wall clock time. Since, I want to check whether
> its
> > > running in serial or parallel.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > With kind regards,
> > G. Sreemol
> > M.Tech (Computational Biology)
> > Anna university
> > Chennai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Mon Apr 04 2016 - 05:00:03 PDT
