Hi Hadrian,
The last problem (compiling pmemd) is now a known issue with the intel
compilers.* It revolves around the -fast optimization flag and the
other flags it is automatically calling (-static) and the type of
libraries you have on your system (looks like dynamic). Try editing
your $AMBERHOME/src/config.h (and $AMBERHOME/AmberTools/src/config.h)
file and replacing '-fast' with '-ipo -O3 -no-prec-div -xHost'. Then
do a "make clean" and recompile the parallel version.
Best,
Paul
*It's not really a bug, you just have to be "heads up" about whether
you've got static or dynamic libraries.
On Oct 3, 2010, at 10:30 PM, Hadrian Djohari wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Oct 03 2010 - 23:00:05 PDT
