Re: amber-developers: Error in parallel installation of AMBER 9

From: Xuebin Qiao <xbqiao.gmail.com>
Date: Tue, 29 Nov 2005 01:24:59 -0700

Hi,

It seems you try to link with MPICH2 library. Check whether you have
installed MPICH2 not MPICH. If not, upgrade to newer version or choose
other configure option. Although I do not have amber9 source, I guess they
still support old -mpich option.

best regards

qxb


On 11/29/05, Ilyas Yildirim < <mailto:yildirim.pas.rochester.edu>
yildirim.pas.rochester.edu> wrote:

Dear All,

I have updated the latest code from chagall and succesfully compiled the
serial version of AMBER 8. When I try to compiled the parallel version,
following the 'parallel installation protocol' I am ending with an error
message as follows:

-------------------------------------------
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
ifort -FR -o sander evb_vars.o evb_ntrfc.o evb_input.o check_input.o
evb_io.o evb_drvr.o evb_keywrd.o exchange_CM.o evb_mcp.o evb_matrix.o
evb_force.o diabatic.o evb_2stdebug.o constants.o stack.o qmmm_module.o
trace.o lmod.o decomp.o icosasurf.o egb.o findmask.o pb_force.o
relax_mat.o
nmr.o multisander.o sander.o trajene.o cshf.o nmrcal.o pearsn.o printe.o
runmin.o force.o rdparm.o mdread.o locmem.o runmd.o getcor.o degcnt.o
decnvh.o fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o set.o
dynlib.o
mdfil.o nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o
nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o rfree.o rgroup.o
random.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
ew_dipole_recip.o
mexit.o new_time.o extra_pts.o thermo_int.o matinv.o assert.o mmtsb.o
mmtsb_client.o erfcfun.o veclib.o pb_init.o constantph.o prn_dipoles.o
neb.o
ips.o sglds.o amoeba_valence.o amoeba_multipoles.o amoeba_recip.o
amoeba_interface.o amoeba_direct.o amoeba_mdin.o amoeba_adjust.o
amoeba_self.o amoeba_vdw.o amoeba_induced.o amoeba_runmd.o bintraj.o
qm_mm.o
qm_link_atoms.o qm_nb_list.o qm_extract_coords.o qm_ewald.o qm_gb.o
qm_zero_charges.o qm_print_info.o qm_assign_atom_types.o
qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_rij_and_eqns.o
qm2_dhc.o
qm2_dihed.o qm2_energy.o qm2_fock.o qm2_get_qm_forces.o
qm2_get_qmmm_forces.o qm2_h1elec.o qm2_hcore_qmqm.o qm2_hcore_qmmm.o
qm2_helect.o qm2_identify_peptide_links.o qm2_load_params_and_allocate.o
qm2_repp.o qm2_rotate_qmqm.o qm2_scf.o qm2_setup_orb_exp.o
qm2_smallest_number.o \
        ../lmod/lmod.a -L/usr/local/mpich/lib -lfmpich2g -lmpi
../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a
ld: cannot find -lfmpich2g
make[1]: *** [sander] Error 1
make[1]: Leaving directory /home/yildirim/amber9/src/sander'
make: *** [parallel] Error 2
arde00:/home/yildirim/amber9/src>

------------------------------------------------------

I could install the parallel ver. before, but not anymore after I have
updated AMBER 9. Can someone tell me what might be the problem? I am
guessing that something in MPICH protocol is changed, or? Thanks.

Best,

--
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  -  <http://www.pas.rochester.edu/%7Eyildirim/>
http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------
-- 
... there have been two really clean, 
consistent models of programming so far: 
the C model and the Lisp model. 
These two seem points of high ground, 
with swampy lowlands between them.
                                      --Paul Graham 
Received on Wed Apr 05 2006 - 23:49:47 PDT
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