Hi everyone,
> I have some difficulty installing Amber 11 in our cluster, so I would
> appreciate everyone's help. I would like the answers to all the questions
> below, but if someone can help me with the answer for the specific
> openmpi/intel installation right at the bottom part, I would be really
> grateful.
>
> Amber installation questions:
>
> 1. The instruction in the Amber and AmberTools document seem to direct
> people to have both the source and the compiled binaries in the same
> directory by using only "make" instead of "make install". Is this the only
> way? We prefer to have the source and the compiled binaries in different
> directories (/usr/local/src/amber and /usr/local/amber). If we want separate
> directories, which one should $AMBERHOME point to?
>
> 2. The installer should be "root" or a user? I compiled "make serial"
> just fine as a user, but found some errors compiling as "root", probably due
> to some paths not being recognized.
>
> 3. Since I'm installing Amber, I should also install AmberTools. And
> I'd like to install the parallel version. So, is there a step-by-step
> instructions on how to install Amber (with AmberTools) as parallel code
> (please see no.1 too)? That would be EXTREMELY HELPFUL. Some of these
> questions needed answers (why do I have to install the serial versions
> first? how do I link to an existing libraries (fftw, mpi, mkl)? what paths
> are needed by the installer to execute?). These small things can lead to an
> unsuccessful compilation, so I would really like some more detailed
> information about this.
>
> 4. Once the code is compiled, is there a short test job that use PBS
> submission, not the "make test" that is available in the directories?
>
>
> Also, I have tried this approach to install MD on a RHEL5.5 server:
export AMBERHOME=/usr/local/amber/amber11
cd $AMBERHOME/AmberTools/src
./configure -mpi intel
make parallel
This is successful.
And then:
cd $AMBERHOME/src
make parallel
But it produces this error;
...
mpif90 -fast -c charmm_gold.f90
mpif90 -fast -o pmemd.MPI gbl_constants.o gbl_datatypes.o state_info.o
file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o
prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel_dat.o parallel.o
gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o
pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o
pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o
dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o
runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o
pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o
degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o
nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o
charmm_gold.o ../../netcdf/lib/libnetcdf.a
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11005: generating object file /tmp/ipo_ifortPoYvAz.o
/usr/bin/ld: cannot find -lmpi_f90
make[2]: *** [pmemd.MPI] Error 1
make[2]: Leaving directory `/usr/local/amber/amber11/src/pmemd/src'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/usr/local/amber/amber11/src/pmemd'
make: *** [parallel] Error 2
I don't know why it cannot find -lmpi_f90 since libmpi_f90.* are in the
directory that is in the ld_library path
hxd58.login:/usr/local/amber/amber11/src$ echo $LD_LIBRARY_PATH
/usr/local/openmpi/openmpi-intel/lib/:/usr/local/lib:/usr/local/intel/compilers/11.1.056/lib/intel64:/usr/local/intel/compilers/11.1.056/idb/lib/intel64
hxd58.login:/usr/local/amber/amber11/src$ ll
/usr/local/openmpi/openmpi-intel/lib
...
-rwxr-xr-x 1 root root 1129 Mar 26 2010 libmpi_f90.la
lrwxrwxrwx 1 root root 19 Mar 26 2010 libmpi_f90.so ->
libmpi_f90.so.0.0.0
lrwxrwxrwx 1 root root 19 Mar 26 2010 libmpi_f90.so.0 ->
libmpi_f90.so.0.0.0
-rwxr-xr-x 1 root root 17140 Mar 26 2010 libmpi_f90.so.0.0.0
...
Thank you,
--
Hadrian Djohari
HPCC Manager
Case Western Reserve University
(W): 216-368-0395
(M): 216-798-7490
--
Hadrian Djohari
HPCC Manager
Case Western Reserve University
(W): 216-368-0395
(M): 216-798-7490
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Received on Sun Oct 03 2010 - 23:00:03 PDT
