AMBER Archive (2003)

Subject: Re: AMBER: Scyld cluster amber 7 compile problems

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Sep 18 2003 - 12:50:08 CDT

Hello,

I built sander 7 with the machine file below
on a P4 with pgcc pgf77 5.0-2, LAM 6.5.7 on
Red Hat Linux release 7.3 (Valhalla)
It passed all the tests.
Your problems are namelist related.
line 142 is
          READ(IIN,WT)

You could try replacing in eg, tgtmd.in,
 &end
with
 /

A google search on namelists with site:structbio.vanderbilt.edu
will provide more tips and tricks for namelist troubles.

Good luck,
Scott Brozell

#! /bin/csh -f
########################################################################
# #
# Copyright (c) 1986, 1991, 1995 #
# Regents of the University of California #
# #
# All Rights Reserved #
# #
# Machine Dependency Handling System #
# #
# Bill Ross ross_at_cgl.ucsf.edu #
# An extension of work of George Seibel #
# #
# Dependencies written by various authors. #
# #
# Permission to use, copy, modify, and distribute this software and #
# its documentation for any purpose and without fee is hereby #
# granted, provided that the above copyright notice appear in all #
# copies and that both that copyright notice and this permission #
# notice appear in supporting documentation, and that the name of #
# the University of California not be used in advertising or #
# publicity pertaining to distribution of the software without #
# specific, written prior permission. #
# #
# THE REGENTS OF THE UNIVERSITY OF CALIFORNIA DISCLAIM ALL #
# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED #
# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE #
# UNIVERSITY OF CALIFORNIA BE LIABLE FOR ANY SPECIAL, INDIRECT OR #
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM #
# LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, #
# NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN #
# CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. #
# #
########################################################################

setenv LAM_INCLUDE $LAM_HOME/include
setenv LAM_LIBDIR $LAM_HOME/lib
setenv LAM_LIB '-llamf77mpi -lmpi -llam'

#
setenv MACHINE "linux/FreeBSD/Windows PC"
setenv MACH Linux
setenv MACHINEFLAGS "-DMPI -DRLE -DROWAT -DMEM_ALLOC"

# CPP is the cpp for this machine
setenv CPP "/lib/cpp -traditional -I$LAM_INCLUDE"

# SYSDIR is the name of the system-specific source directory relative to src/*/
setenv SYSDIR Machines/standard

# COMPILER ALIASES:
setenv CC "pgcc "
setenv FC "pgf90 "
setenv PG_OPT "-O2 -Munroll -tp piv -Mnoframe -Msecond_underscore -Mvect -Mvect=sse"
setenv OPT_0 "-O0 -tp piv -Mnoframe -Msecond_underscore"
setenv OPT_1 "$PG_OPT"
setenv OPT_2 "$PG_OPT"
setenv OPT_3 "$PG_OPT"

# LOADER/LINKER:
setenv LOAD "pgf90 -Bstatic "
setenv LOADCC "pgcc -Bstatic "
setenv LOADLIB " -L$LAM_LIBDIR $LAM_LIB -lm "

#setenv G77_COMPAT "-fno-globals -ff90 -funix-intrinsics-hide"
#
# following seems to actually slow down code, though it works well on CHARMM:
#setenv G77_OPT "-O6 -m486 -malign-double -ffast-math -fomit-frame-pointer -funroll-loops -funroll-all-loops -mcpu=pentiumpro -march=pentiumpro -ffloat-store -fforce-mem -frerun-cse-after-loop -fexpensive-optimizations -fugly-complex"

# following appears to be the best we have found so far:
setenv G77_OPT "-O3 -m486 -malign-double -ffast-math -fomit-frame-pointer"

# little or no optimization:
setenv L0 "$FC -c $OPT_0"

# modest optimization (local scalar):
setenv L1 "$FC -c $OPT_1"

# high scalar optimization (but not vectorization):
setenv L2 "$FC -c $OPT_2"

# high optimization (may be vectorization, not parallelization):
setenv L3 "$FC -c $OPT_3"

# ranlib, if it exists
setenv RANLIB ranlib

On Wed, 17 Sep 2003, Bengt Svensson wrote:

> I have been trying to install Amber 7 on a Sculd Linux cluster, but are
> having some problems.
>
> The cluster is 4 dual AMD Athlon MP 2600+ (total 8 cpu), 2GB memory
> per node, with gigabit ethernet connection.
> It is running Scyld 28cz5.1 (Based off RedHat 7.1?), gcc 2.96, pgf77 5.0-2,
> and mpich 1.2.3.
>
>
> The source code for amber 7 has been patched with bugfix 1-39.
>
>
> I have followed the instruction and used the Machine files from:
>
> http://amber.scripps.edu/cluster_info/index.html
>
> I did the following modifications to reflect the location of the MPICH
> libraries and SYSDIR
>
> #setenv MPICH_HOME /usr/lib/mpich
> setenv MPICH_HOME /usr
>
> #setenv SYSDIR Machines/g77
> setenv SYSDIR Machines/standard
>
>
> I tried both to compile with pgf77 and g77, serial and parallel (mpi)
> versions.
>
> When I compile with pgf77 everything seems to be going fine. No warnings.
>
> I run the test.sander and I get errors on the following tests (see below).
> Most tests ran just fine. This happened with both the serial and
> parallel versions.
>
> Compilation with g77 gives quite a few warnings, but completes.
> test.sander works just fine, all tests are passed.
>
> What is the cause of these errors with pgf77? Do anyone have any
> suggestions?
>
> Thanks,
>
> Bengt Svensson
>
>
> ***pgf77 serial***
>
> cd tgtmd/change_target; ./Run.tgtmd
> SANDER: Targeted MD with changing target
> PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
> File name = tgtmd.in formatted, sequential access record = 16
> In source file _restal_.f, at line number 142
> Program error
> make: *** [test.sander] Error 1
>
>
> ***pgf77 parallel (mpich)***
>
> cd tgtmd/change_target; ./Run.tgtmd
> SANDER: Targeted MD with changing target
> PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
> File name = tgtmd.in formatted, sequential access record = 16
> In source file _restal_.f, at line number 142
> p3_2705: p4_error: net_recv read: probable EOF on socket: 1
> p2_2703: p4_error: net_recv read: probable EOF on socket: 1
> p1_2702: p4_error: net_recv read: probable EOF on socket: 1
> bm_list_2701: (0.140309) net_send: could not write to fd=5, errno = 9
> bm_list_2701: p4_error: net_send write: -1
> p4_error: latest msg from perror: Bad file descriptor
> Program error
> make: *** [test.sander] Error 1
>
> cd tgtmd/PME; ./Run.tgtPME
> SANDER: Targeted MD with PME
> PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
> File name = tgtmd.in formatted, sequential access record = 23
> In source file _restal_.f, at line number 142
> p3_4277: p4_error: net_recv read: probable EOF on socket: 1
> p2_4275: p4_error: net_recv read: probable EOF on socket: 1
> p1_4274: p4_error: net_recv read: probable EOF on socket: 1
> bm_list_4273: (0.141386) net_send: could not write to fd=5, errno = 9
> bm_list_4273: p4_error: net_send write: -1
> p4_error: latest msg from perror: Bad file descriptor
> Program error
> make: *** [test.sander] Error 1
>
>
>
>
>
> ------------------------------------------------------------------------------
> Dr. Bengt Svensson
> University Of Minnesota e-mail: bsven_at_msi.umn.edu
> Dept. of Medicinal Chemistry tel: +1-612-626-4429
> 8-101 Weaver-Densford Hall fax: +1-612-626-4429
> 308 Harvard St. SE
> Minneapolis, MN 55455
> USA Visiting addr: 7-125D Weaver-Densford Hall
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu