AMBER Archive (2009)

Subject: [AMBER] hpux sander.serial failure info

From: Yiannis Georgiadis (giannis_at_cc.uoa.gr)
Date: Thu Apr 09 2009 - 17:28:28 CDT

I send you from Univ of Athens more detailed info
on resolving sander building failure - bus error in many situations-

There are below the attached tests.out -after issuing a make test
command-
and config_amber.h created by running configure with hpf90 compiler
option

thanks in advance for your help

Yiannis Georgiadis


#==============================================================================
# AMBER Makefile configuration for compiler/architecture: hpf90
# Generated via command: ./configure_amber hpf90
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================

#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=

#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=

#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(VENDOR_SUPPLIED)
USE_LAPACKLIB=$(VENDOR_SUPPLIED)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= cc
CPLUSPLUS=aCC
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Ae -DSYSV $(AMBERBUILDFLAGS)
CPPFLAGS=-DCLINK_PLAIN -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -DHP -DBINTRAJ $(AMBERBUILDFLAGS)
FPP= /lib/cpp $(FPPFLAGS)
FC= f90
FFLAGS= +noppu +U77 +Ofast $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= +noppu +U77 +Ofast $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= +source=free

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= f90 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= cc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -lveclib -llapack -lm
LM= -lm
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
EMPTY=
AR=ar rvs $(EMPTY)
M4=m4 -B50000
RANLIB=/bin/true
SFX=
NETCDF=netcdf.mod
NETCDFLIB=../netcdf/lib/libnetcdf.a
MODULEDIR=-I
testsanderDIVCON=test.sander.DIVCON
INCDIVCON=divcon
LIBDIVCON=../dcqtp/src/qmmm/libdivcon.a

# Location for executables, etc:

BINDIR=/inc/tmp/amber10/bin
LIBDIR=/inc/tmp/amber10/lib
INCDIR=/inc/tmp/amber10/include
DATDIR=/inc/tmp/amber10/dat

# default rules for Fortran and C compilation:

.f.o: $<
        $(FPP) $< > _$<
        $(FC) -c $(FFLAGS) -o $@ _$<

.c.o:
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<


(find . -name '*.dif' -o -name 'profile_mpi' | \
        while read dif ;\
        do \
            rm -f $dif ;\
        done ;\
        )
rm -f TEST_FAILURES.diff
cd dmp && ./Run.dmp
diffing mdout.dmp.save with mdout.dmp
PASSED
==============================================================
cd adenine && ./Run.adenine
diffing mdout.adenine.save with mdout.adenine
PASSED
==============================================================
cd cytosine && ./Run.cytosine
Bus error (core dumped)
  ./Run.cytosine: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd nonper && ./Run.nonper
Bus error (core dumped)
  ./Run.nonper: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd nonper && ./Run.nonper.belly
Bus error (core dumped)
  ./Run.nonper.belly: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd nonper && ./Run.nonper.belly.mask
Bus error (core dumped)
  Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd nonper && ./Run.nonper.min
diffing mdout.min.save with mdout.min
PASSED
==============================================================
cd nonper && ./Run.cap
Bus error (core dumped)
  ./Run.cap: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd nonper && ./Run.nonper.nocut
Bus error (core dumped)
  ./Run.nonper.nocut: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tip4p && ./Run.tip4p
Bus error (core dumped)
  ./Run.tip4p: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tip4p && ./Run.tip4p_nve
Bus error (core dumped)
  ./Run.tip4p_nve: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tip5p && ./Run.tip5p
Bus error (core dumped)
  ./Run.tip5p: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tip5p && ./Run.tip5p_nve
Bus error (core dumped)
  ./Run.tip5p_nve: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd 4096wat && ./Run.pure_wat
Bus error (core dumped)
  ./Run.pure_wat: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd 4096wat && ./Run.pure_wat_nmr_temp_reg
Segmentation fault (core dumped)
  ./Run.pure_wat_nmr_temp_reg: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd 4096wat && ./Run.vrand
Bus error (core dumped)
  ./Run.vrand: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd dhfr && ./Run.dhfr
Bus error (core dumped)
  ./Run.dhfr: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd dhfr && ./Run.dhfr.noshake
Bus error (core dumped)
  ./Run.dhfr.noshake: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd dhfr && ./Run.dhfr.min
diffing mdout.dhfr.min.save with mdout.dhfr.min
PASSED
==============================================================
cd gact_ips && ./Run.ips
Bus error (core dumped)
  ./Run.ips: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd gact_ips && ./Run.ipsnve
Bus error (core dumped)
  ./Run.ipsnve: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd gact_ips && ./Run.ips_sgld
Bus error (core dumped)
  ./Run.ips_sgld: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd polarizable_water && ./Run.pol_wat
Bus error (core dumped)
  ./Run.pol_wat: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd ubiquitin && ./Run.ubiquitin
Bus error (core dumped)
  ./Run.ubiquitin: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd dna_pol && ./Run.dna_pol
Bus error (core dumped)
  ./Run.dna_pol: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd trx && ./Run.trx
Bus error (core dumped)
  ./Run.trx: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd trx && ./Run.trx.cpln
Bus error (core dumped)
  ./Run.trx.cpln: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd rdc && ./Run.dip
  ./Run.dip: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd rdc && ./Run.csa
diffing gcg.csa.o.save with gcg.csa.o
PASSED
==============================================================
cd rdc && ./Run.csa_min
diffing gcg.csa_min.o.save with gcg.csa_min.o
possible FAILURE: check gcg.csa_min.o.dif
==============================================================
cd pcsa && ./Run.dip
diffing stem.dip.o.save with stem.dip.o
PASSED
==============================================================
cd pcsa && ./Run.csa
diffing stem.csa.o.save with stem.csa.o
PASSED
==============================================================
cd pcsa && ./Run.csa2
diffing stem.csa2.o.save with stem.csa2.o
PASSED
==============================================================
cd pcsa && ./Run.csa_min
diffing stem.csa_min.o.save with stem.csa_min.o
possible FAILURE: check stem.csa_min.o.dif
==============================================================
cd tgtmd/change_target && ./Run.tgtmd
SANDER: Targeted MD with changing target
Bus error (core dumped)
  ./Run.tgtmd: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tgtmd/change_target.rms && ./Run.tgtmd
SANDER: Targeted MD with changing target and fit/rmsd
        to different regions
Bus error (core dumped)
  ./Run.tgtmd: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tgtmd/change_target.ntr && ./Run.tgtmd
SANDER: Targeted MD with changing target and restraints
Bus error (core dumped)
  ./Run.tgtmd: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tgtmd/conserve_ene && ./Run.tgtmd
SANDER: Targeted MD energy conservation test
Bus error (core dumped)
  ./Run.tgtmd: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd tgtmd/minimize && ./Run.tgtmin
SANDER: Targeted minimization
diffing tgtmin.out.save with tgtmin.out
possible FAILURE: check tgtmin.out.dif
==============================================================
cd tgtmd/PME && ./Run.tgtPME
SANDER: Targeted MD with PME
Bus error (core dumped)
  ./Run.tgtPME: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd trajene && ./Run.trajene
diffing trajene.out.save with trajene.out
PASSED
==============================================================
cd alp && ./Run.alp
Bus error (core dumped)
  ./Run.alp: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd pb_pgb && ./Run.pbpgb
Bus error (core dumped)
  ./Run.pbpgb: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd umbrella && ./Run.umbrella
Segmentation fault (core dumped)
  ./Run.umbrella: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd noesy && ./Run.noesy
  ./Run.noesy: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd jar && ./Run.jar
Segmentation fault (core dumped)
  ./Run.jar: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd plane_plane_restraint && ./Run.dinuc_plpt
SANDER: Dinucleoside restrained with new plane-point angle
        restraint that was defined with new natural
        language restraint input.
Segmentation fault (core dumped)
  ./Run.dinuc_plpt: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd plane_plane_restraint && ./Run.dinuc_pln
SANDER: Dinucleoside restrained with new plane-plane angle
        restraint that was defined with new natural
        language restraint input.
Bus error (core dumped)
  ./Run.dinuc_pln: Program error
gmake: [test.sander.BASIC] Error 1 (ignored)
cd bintraj && ./Run.bintraj
Bus error (core dumped)
diffing nc_headers.save with nc_headers
possible FAILURE: check nc_headers.dif
==============================================================
cd gb_rna && ./Run.gbrna
Bus error (core dumped)
  ./Run.gbrna: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd gb_rna && ./Run.gbrna.min
diffing mdout.gbrna.min.save with mdout.gbrna.min
PASSED
==============================================================
cd gb_rna && ./Run.gbrna.ln
Bus error (core dumped)
  ./Run.gbrna.ln: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd gb_rna && ./Run.gbrna.ips
Bus error (core dumped)
  ./Run.gbrna.ips: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd gb_rna && ./Run.gbrna.sgld
Bus error (core dumped)
  ./Run.gbrna.sgld: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd gbsa_xfin && ./Run.gbsa
Segmentation fault (core dumped)
  ./Run.gbsa: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd circ_dna && ./Run.circdna
diffing mdout.circdna.save with mdout.circdna
PASSED
==============================================================
cd gb2_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd gb7_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd gb7_trx && ./Run.trxox_md
Bus error (core dumped)
  ./Run.trxox_md: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd alpb_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd cnstph && ./Run.cnstph
Bus error (core dumped)
  ./Run.cnstph: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd gb1_cox2 && ./Run.cox2
Segmentation fault (core dumped)
  ./Run.cox2: Program error
gmake: [test.sander.GB] Error 1 (ignored)
cd LES_noPME && ./Run.LESmd
SANDER: LES MD gas phase
diffing md.out.save with md.out
PASSED
==============================================================
cd LES_noPME && ./Run.LESmd.rdiel
SANDER: LES MD gas phase rdiel
diffing md.rdiel.out.save with md.rdiel.out
PASSED
==============================================================
cd LES && ./Run.PME_LES
 
  Amber 8 ADDLES and SANDER.LES test:
 
addles:
  ./Run.PME_LES: Program error
gmake: [test.sander.LES] Error 1 (ignored)
cd LES_CUT && ./Run.LES
 
  Amber 10 SANDER.LES test, no PME
 
diffing md.LES.out.save with md.LES.out
PASSED
==============================================================
cd LES_GB && ./Run.LES
SANDER: LES+GB
1: GB/LES GB1 diffcoords
diffing les.gb1.diffcrd.out.save with les.gb1.diffcrd.out
PASSED
==============================================================
1: GB/LES GB1 samecoords
diffing les.gb1.samecrd.out.save with les.gb1.samecrd.out
PASSED
==============================================================
1: GB/LES GB5 samecoords
diffing les.gb5.samecrd.out.save with les.gb5.samecrd.out
PASSED
==============================================================
1: GB/LES GB7 samecoords
diffing les.gb7.samecrd.out.save with les.gb7.samecrd.out
PASSED
==============================================================
1: GB/LES GB7 diffcoords w/RDT
diffing les.gb7.rdt.out.save with les.gb7.rdt.out
PASSED
==============================================================
cd PIMD/part_pimd_water && ./Run.pimd
diffing addles.out.save with addles.out
awk: Cannot find or open file /dev/stderr.
 The source line number is 656.
possible FAILURE: check addles.out.dif
==============================================================
diffing pimd.out.save with pimd.out
PASSED
==============================================================
cd PIMD/part_nmpimd_water && ./Run.nmpimd
diffing nmpimd.out.save with nmpimd.out
PASSED
==============================================================
cd PIMD/part_pimd_helium && ./Run.pimd
diffing hef_pimd.out.save with hef_pimd.out
PASSED
==============================================================
cd PIMD/part_nmpimd_helium && ./Run.nmpimd
diffing hef_pimd.out.save with hef_pimd.out
PASSED
==============================================================
cd PIMD/part_nmpimd_ntp && ./Run.nmpimd
diffing ntp_nmpimd.out.save with ntp_nmpimd.out
PASSED
==============================================================
diffing NHC.dat.save with NHC.dat
PASSED
==============================================================
cd PIMD/part_pimd_spcfw && ./Run.pimd
  ./Run.pimd: Program error
gmake: [test.sander.PIMD.partial] Error 1 (ignored)
cd PIMD/part_cmd_water/equilib && ./Run.cmdyn
  ./Run.cmdyn: Program error
gmake: [test.sander.PIMD.partial] Error 1 (ignored)
cd PIMD/part_cmd_water/start && ./Run.cmdyn
diffing cmd.out.save with cmd.out
PASSED
==============================================================
cd PIMD/part_cmd_water/restart && ./Run.cmdyn
diffing cmd.out.save with cmd.out
PASSED
==============================================================
cd PIMD/part_rpmd_water && ./Run.rpmd
  ./Run.rpmd: Program error
gmake: [test.sander.PIMD.partial] Error 1 (ignored)
cd ti_mass/pent_LES_PIMD && ./Run.pentadiene
  ./Run.pentadiene: Program error
gmake: [test.sander.PIMD.partial] Error 1 (ignored)
cd amoeba_wat1 && ./Run.amoeba_wat1
Bus error (core dumped)
  ./Run.amoeba_wat1: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd amoeba_wat2 && ./Run.amoeba_wat2
Bus error (core dumped)
  ./Run.amoeba_wat2: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd amoeba_wat2 && ./Run.ntpverlet
Segmentation fault (core dumped)
  ./Run.ntpverlet: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd amoeba_gb1 && ./Run.amoeba_gb1
Bus error (core dumped)
  ./Run.amoeba_gb1: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd amoeba_jac && ./Run.amoeba_jac
Bus error (core dumped)
  ./Run.amoeba_jac: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd amoeba_formbox && ./Run.amoeba_formbox
Bus error (core dumped)
  ./Run.amoeba_formbox: Program error
gmake: [test.sander.AMOEBA] Error 1 (ignored)
cd ncsu && ./run-serial.sh
>>>>>>> doing 'abmd_ANALYSIS'
./run.sh[37]: 7247 Bus error(coredump)
diffing save/mdout with mdout
possible FAILURE: check mdout.dif
==============================================================
cat: Cannot open monitor.txt: No such file or directory
diffing save/monitor.txt with monitor.txt
possible FAILURE: check monitor.txt.dif
==============================================================
>>>>>>> doing 'abmd_FLOODING'
./run.sh[37]: 7313 Bus error(coredump)
diffing save/mdout with mdout
possible FAILURE: check mdout.dif
==============================================================
cat: Cannot open monitor.txt: No such file or directory
diffing save/monitor.txt with monitor.txt
possible FAILURE: check monitor.txt.dif
==============================================================
/inc/tmp/amber10/src/netcdf/bin/ncdump: umbrella.nc: No such file or directory
ncgen: -: syntax error
/inc/tmp/amber10/src/netcdf/bin/ncdump: ncdump.tmp: No such file or directory
diffing umbrella.save.ncdump with umbrella.ncdump
possible FAILURE: check umbrella.ncdump.dif
==============================================================
>>>>>>> doing 'abmd_UMBRELLA'
./run.sh[37]: 7427 Bus error(coredump)
diffing save/mdout with mdout
possible FAILURE: check mdout.dif
==============================================================
cat: Cannot open monitor.txt: No such file or directory
diffing save/monitor.txt with monitor.txt
possible FAILURE: check monitor.txt.dif
==============================================================
>>>>>>> doing 'smd'
./run.sh[27]: 7494 Bus error(coredump)
diffing save/mdout with mdout
possible FAILURE: check mdout.dif
==============================================================
cat: Cannot open smd.txt: No such file or directory
diffing save/smd.txt with smd.txt
possible FAILURE: check smd.txt.dif
==============================================================
>>>>>>> doing 'pmd'
./run.sh[27]: 7561 Bus error(coredump)
diffing save/mdout with mdout
possible FAILURE: check mdout.dif
==============================================================
cat: Cannot open pmd.txt: No such file or directory
diffing save/pmd.txt with pmd.txt
possible FAILURE: check pmd.txt.dif
==============================================================
cd nmode && ./Run.ala-dipeptide
 
NMODE: find normal modes
diffing vibs.out.save with vibs.out
PASSED
==============================================================
 
NMODE: find Langevin modes
diffing lvibs.out.save with lvibs.out
PASSED
==============================================================
diffing lmode.head.save with lmode.head
PASSED
==============================================================
 
cd nmode && ./Run.ala-dipeptide_rgroup
 
NMODE: find normal modes, with a restraint weighting
diffing vibsr.out.save with vibsr.out
PASSED
==============================================================
cd newton_raph && ./Run.newton_raph
diffing nmd_min.out.save with nmd_min.out
PASSED
==============================================================
cd pbsa_trx && ./Run.trxox.min
diffing mdout.trxox.min.save with mdout.trxox.min
PASSED
==============================================================
cd pbsa_dmp && ./Run.dmp.min
diffing mdout.dmp.min.save with mdout.dmp.min
PASSED
==============================================================
cd pbsa_pgb && ./Run.pbpgb.min
diffing mdout.pbpgb.min.save with mdout.pbpgb.min
PASSED
==============================================================
cd pbsa_radi && ./Run.ion.min
diffing ./out.save/Li.out.save with Li.out
PASSED
==============================================================
diffing ./out.save/Na.out.save with Na.out
PASSED
==============================================================
diffing ./out.save/K.out.save with K.out
PASSED
==============================================================
diffing ./out.save/Rb.out.save with Rb.out
PASSED
==============================================================
diffing ./out.save/Cs.out.save with Cs.out
PASSED
==============================================================
diffing ./out.save/F.out.save with F.out
PASSED
==============================================================
diffing ./out.save/Cl.out.save with Cl.out
PASSED
==============================================================
diffing ./out.save/IM.out.save with IM.out
PASSED
==============================================================
diffing ./out.save/Br.out.save with Br.out
PASSED
==============================================================
diffing ./out.save/I.out.save with I.out
PASSED
==============================================================
diffing ./out.save/MG.out.save with MG.out
PASSED
==============================================================
diffing ./out.save/Ca.out.save with Ca.out
PASSED
==============================================================
diffing ./out.save/Zn.out.save with Zn.out
PASSED
==============================================================
diffing ./out.save/tp3.out.save with tp3.out
PASSED
==============================================================
diffing ./out.save/ile.out.save with ile.out
PASSED
==============================================================
diffing ./out.save/leu.out.save with leu.out
PASSED
==============================================================
diffing ./out.save/val.out.save with val.out
PASSED
==============================================================
diffing ./out.save/phe.out.save with phe.out
PASSED
==============================================================
diffing ./out.save/trp.out.save with trp.out
PASSED
==============================================================
diffing ./out.save/hid.out.save with hid.out
PASSED
==============================================================
diffing ./out.save/hie.out.save with hie.out
PASSED
==============================================================
diffing ./out.save/nhe.out.save with nhe.out
PASSED
==============================================================
diffing ./out.save/tyr.out.save with tyr.out
PASSED
==============================================================
diffing ./out.save/ser.out.save with ser.out
PASSED
==============================================================
diffing ./out.save/thr.out.save with thr.out
PASSED
==============================================================
diffing ./out.save/cys.out.save with cys.out
PASSED
==============================================================
diffing ./out.save/cyx.out.save with cyx.out
PASSED
==============================================================
diffing ./out.save/met.out.save with met.out
PASSED
==============================================================
diffing ./out.save/lyn.out.save with lyn.out
PASSED
==============================================================
diffing ./out.save/ash.out.save with ash.out
PASSED
==============================================================
diffing ./out.save/glh.out.save with glh.out
PASSED
==============================================================
diffing ./out.save/asn.out.save with asn.out
PASSED
==============================================================
diffing ./out.save/gln.out.save with gln.out
PASSED
==============================================================
diffing ./out.save/nma.out.save with nma.out
PASSED
==============================================================
diffing ./out.save/alabk.out.save with alabk.out
PASSED
==============================================================
diffing ./out.save/glybk.out.save with glybk.out
PASSED
==============================================================
diffing ./out.save/probk.out.save with probk.out
PASSED
==============================================================
diffing ./out.save/da.out.save with da.out
PASSED
==============================================================
diffing ./out.save/dc.out.save with dc.out
PASSED
==============================================================
diffing ./out.save/dg.out.save with dg.out
PASSED
==============================================================
diffing ./out.save/dt.out.save with dt.out
PASSED
==============================================================
diffing ./out.save/ru.out.save with ru.out
PASSED
==============================================================
diffing ./out.save/arg.out.save with arg.out
PASSED
==============================================================
diffing ./out.save/asp.out.save with asp.out
PASSED
==============================================================
diffing ./out.save/cym.out.save with cym.out
PASSED
==============================================================
diffing ./out.save/glu.out.save with glu.out
PASSED
==============================================================
diffing ./out.save/hip.out.save with hip.out
PASSED
==============================================================
diffing ./out.save/lys.out.save with lys.out
PASSED
==============================================================
diffing ./out.save/dap.out.save with dap.out
PASSED
==============================================================
diffing ./out.save/da3p.out.save with da3p.out
PASSED
==============================================================
diffing ./out.save/da5p.out.save with da5p.out
PASSED
==============================================================
diffing ./out.save/danp.out.save with danp.out
PASSED
==============================================================
diffing ./out.save/rap.out.save with rap.out
PASSED
==============================================================
diffing ./out.save/ra3p.out.save with ra3p.out
PASSED
==============================================================
diffing ./out.save/ra5p.out.save with ra5p.out
PASSED
==============================================================
diffing ./out.save/ranp.out.save with ranp.out
PASSED
==============================================================
cd pbsa_tsr && ./Run.tsrb.min
diffing mdout.tsrb.min.save with mdout.tsrb.min
PASSED
==============================================================
cd pbsa_decres && ./Run.pbsa_decres
diffing mdout.pbsa_decres.save with mdout.pbsa_decres
PASSED
==============================================================
cd pbsa_decpw && ./Run.pbsa_decpw
diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw
PASSED
==============================================================
cd ambpdb && ./Run.ambpdb
diffing restrt.pdb.save with restrt.pdb
PASSED
==============================================================
cd ambpdb_first_protein && ./Run.ambpdb
diffing first.pdb.save with first.pdb
possible FAILURE: check first.pdb.dif
==============================================================
cd ambpdb_first_rna && ./Run.ambpdb
diffing first.pdb.save with first.pdb
possible FAILURE: check first.pdb.dif
==============================================================
cd elsize && ./Run.elsize
diffing elsize_out.trxox.save with elsize_out.trxox
PASSED
==============================================================
Finished serial test suite for the MM portions of Amber 10;
to test QM/MM, type 'make test.serial.QMMM'

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber