AMBER Archive (2008)

Subject: Re: AMBER: Installation problem of AMBER on cluster

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Sat May 03 2008 - 00:59:23 CDT

Hi Ross,

       At last I have successfully installed static version of MPICH2 under
your guidence. But still the problems are remaining. Now the issues are
coming from AMBER installation. I set the environment variable (AMBERHOME,
MPI_HOME, PATH ) in the .bashrc file. Then I have done the following
steps which you told in your earlier mail. But the errors are not clear to
me. Please give some needful help.

 * $./configure -static -mpich2 g95*

ERRORS============================================

AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: g95
Using parallel communications library: mpich2
MPI_HOME is set to /usr/local/mpich2-1.0.7-g95/
The MKL_HOME environment variable is not defined.

The configuration file, config.h, was successfully created.
===================================================

I have not set the MKL_HOME environment variable. How to set this
environment variable? We couldn't find /opt/intel/mkl/8.0 in our machine.
Is this environment variable setting mandatory.

*$make clean*

ERRORS===============================================
cd lib; make clean
make[1]: Entering directory `/usr/local/amber9/src/lib'
/bin/rm malloc_test new2oldparm *.o _*.f *.a
/bin/rm: cannot remove `malloc_test': No such file or directory
/bin/rm: cannot remove `new2oldparm': No such file or directory
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/lib'
cd blas; make clean
make[1]: Entering directory `/usr/local/amber9/src/blas'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o blas.a _*.f
make[1]: Leaving directory `/usr/local/amber9/src/blas'
cd lapack; make clean
make[1]: Entering directory `/usr/local/amber9/src/lapack'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o lapack.a _*.f
make[1]: Leaving directory `/usr/local/amber9/src/lapack'
cd lmod; make clean
make[1]: Entering directory `/usr/local/amber9/src/lmod'
/bin/rm -f *.a
cd xmin; make clean
make[2]: Entering directory `/usr/local/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o _*.f
make[2]: Leaving directory `/usr/local/amber9/src/lmod/xmin'
cd lmod; make clean
make[2]: Entering directory `/usr/local/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o _*.f
make[2]: Leaving directory `/usr/local/amber9/src/lmod/lmod'
make[1]: Leaving directory `/usr/local/amber9/src/lmod'
cd arpack; make clean
make[1]: Entering directory `/usr/local/amber9/src/arpack'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o _*.f arpack.a
make[1]: Leaving directory `/usr/local/amber9/src/arpack'
cd addles; make clean
make[1]: Entering directory `/usr/local/amber9/src/addles'
/bin/rm *.o _*.f addles
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `addles': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/addles'
cd sander; make clean
make[1]: Entering directory `/usr/local/amber9/src/sander'
/bin/rm sander sander.LES psander sander.PIMD
/bin/rm: cannot remove `sander': No such file or directory
/bin/rm: cannot remove `sander.LES': No such file or directory
/bin/rm: cannot remove `psander': No such file or directory
/bin/rm: cannot remove `sander.PIMD': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm ambmask
/bin/rm: cannot remove `ambmask': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm: cannot remove `*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm _*.f
/bin/rm: cannot remove `_*.f': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.mod
/bin/rm: cannot remove `*.mod': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.d
/bin/rm: cannot remove `*.d': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *nbflag
/bin/rm: cannot remove `*nbflag': No such file or directory
make[1]: [clean] Error 1 (ignored)
cd ../dcqtp; make clean
make[2]: Entering directory `/usr/local/amber9/src/dcqtp'
cd mod; make clean
make[3]: Entering directory `/usr/local/amber9/src/dcqtp/mod'
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
make[3]: Leaving directory `/usr/local/amber9/src/dcqtp/mod'
make[2]: Leaving directory `/usr/local/amber9/src/dcqtp'
make[1]: Leaving directory `/usr/local/amber9/src/sander'
cd dcqtp; make clean
make[1]: Entering directory `/usr/local/amber9/src/dcqtp'
cd mod; make clean
make[2]: Entering directory `/usr/local/amber9/src/dcqtp/mod'
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
make[2]: Leaving directory `/usr/local/amber9/src/dcqtp/mod'
make[1]: Leaving directory `/usr/local/amber9/src/dcqtp'
cd ptraj; make clean
make[1]: Entering directory `/usr/local/amber9/src/ptraj'
cd pdb; make clean
make[2]: Entering directory `/usr/local/amber9/src/ptraj/pdb'
rm -f pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o
libpdb.a
make[2]: Leaving directory `/usr/local/amber9/src/ptraj/pdb'
/bin/rm -f main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o
experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o rdparm ptraj
/bin/rm _*.f
/bin/rm: cannot remove `_*.f': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/ptraj'
cd nmr_aux; make clean
make[1]: Entering directory `/usr/local/amber9/src/nmr_aux'
cd prepare_input; make clean
make[2]: Entering directory `/usr/local/amber9/src/nmr_aux/prepare_input'
/bin/rm *.o _*.f makeDIST_RST makeANG_RST makeSHF.cp makeCHIR_RST.cp \
        makeDIP_RST.protein.cp makeDIP_RST.dna.cp
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `makeDIST_RST': No such file or directory
/bin/rm: cannot remove `makeANG_RST': No such file or directory
/bin/rm: cannot remove `makeSHF.cp': No such file or directory
/bin/rm: cannot remove `makeCHIR_RST.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.protein.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.dna.cp': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/nmr_aux/prepare_input'
cd fantasian; make clean
make[2]: Entering directory `/usr/local/amber9/src/nmr_aux/fantasian'
/bin/rm *.o _*.f fantasian
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `fantasian': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/nmr_aux/fantasian'
make[1]: Leaving directory `/usr/local/amber9/src/nmr_aux'
cd nmode; make clean
make[1]: Entering directory `/usr/local/amber9/src/nmode'
/bin/rm *.o _*.f nmode nmanal
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `nmode': No such file or directory
/bin/rm: cannot remove `nmanal': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/nmode'
cd resp; make clean
make[1]: Entering directory `/usr/local/amber9/src/resp'
/bin/rm *.o _*.f resp reformat replace_charges
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `resp': No such file or directory
/bin/rm: cannot remove `reformat': No such file or directory
/bin/rm: cannot remove `replace_charges': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/resp'
cd protonate; make clean
make[1]: Entering directory `/usr/local/amber9/src/protonate'
/bin/rm *.o _*.f pol_h protonate gwh
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `pol_h': No such file or directory
/bin/rm: cannot remove `protonate': No such file or directory
/bin/rm: cannot remove `gwh': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/protonate'
cd etc; make clean
make[1]: Entering directory `/usr/local/amber9/src/etc'
/bin/rm *.o _*.f ambpdb nucgen elsize
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `ambpdb': No such file or directory
/bin/rm: cannot remove `nucgen': No such file or directory
/bin/rm: cannot remove `elsize': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/etc'
cd antechamber; make clean
make[1]: Entering directory `/usr/local/amber9/src/antechamber'
rm -f *.o am1bcc antechamber atomtype bondtype charmmgen crdgrow database
espgen parmcal parmchk prepgen respgen top2mol2 translate
make[1]: Leaving directory `/usr/local/amber9/src/antechamber'
cd mm_pbsa; make clean
make[1]: Entering directory `/usr/local/amber9/src/mm_pbsa'
/bin/rm *.o _*.f make_crd_hg molsurf
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `make_crd_hg': No such file or directory
/bin/rm: cannot remove `molsurf': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/mm_pbsa'
cd pbsa; make clean
make[1]: Entering directory `/usr/local/amber9/src/pbsa'
/bin/rm pbsa
/bin/rm: cannot remove `pbsa': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm: cannot remove `*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm _*.f
/bin/rm: cannot remove `_*.f': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.mod
/bin/rm: cannot remove `*.mod': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.d
/bin/rm: cannot remove `*.d': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/pbsa'
cd anal; make clean
make[1]: Entering directory `/usr/local/amber9/src/anal'
/bin/rm *.o _*.f anal
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `anal': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/anal'
cd leap; make clean
make[1]: Entering directory `/usr/local/amber9/src/leap'
cd src/Wc; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Wc'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Wc'
cd src/Xmu; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xmu'
Makefile:122: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xmu'
cd src/Xpm; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xpm'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xpm'
cd src/Xraw; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xraw'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xraw'
cd src/leap; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/leap'
Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o xaLeap teLeap utilMakeHelp utilDescribeTopology utilCrd2Off
mol2_to_off utilConvertWaterBox utilLib2Pdb *\~
/bin/rm: cannot remove `*.o': No such file or directory
/bin/rm: cannot remove `xaLeap': No such file or directory
/bin/rm: cannot remove `teLeap': No such file or directory
/bin/rm: cannot remove `utilMakeHelp': No such file or directory
/bin/rm: cannot remove `utilDescribeTopology': No such file or directory
/bin/rm: cannot remove `utilCrd2Off': No such file or directory
/bin/rm: cannot remove `mol2_to_off': No such file or directory
/bin/rm: cannot remove `utilConvertWaterBox': No such file or directory
/bin/rm: cannot remove `utilLib2Pdb': No such file or directory
/bin/rm: cannot remove `*~': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm XaLeap_wcl
/bin/rm: cannot remove `XaLeap_wcl': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm *.gprof
/bin/rm: cannot remove `*.gprof': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm parser.c
/bin/rm: cannot remove `parser.c': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm helptext.c
/bin/rm: cannot remove `helptext.c': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/leap'
make[1]: Leaving directory `/usr/local/amber9/src/leap'
cd pmemd; make clean
make[1]: Entering directory `/usr/local/amber9/src/pmemd'
cd src && rm -f *.f90 *.o *.mod pmemd *.d work.pc*
make[1]: Leaving directory `/usr/local/amber9/src/pmemd'
cd build_amoeba; make clean
make[1]: Entering directory `/usr/local/amber9/src/build_amoeba'
/bin/rm amoeba_parm new_crd_to_dyn new_to_old_crd
/bin/rm: cannot remove `amoeba_parm': No such file or directory
/bin/rm: cannot remove `new_crd_to_dyn': No such file or directory
/bin/rm: cannot remove `new_to_old_crd': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm amoeba_parm.f new_crd_to_dyn.f new_to_old_crd.f fix_new_inpcrd_vel.f
/bin/rm: cannot remove `amoeba_parm.f': No such file or directory
/bin/rm: cannot remove `new_crd_to_dyn.f': No such file or directory
/bin/rm: cannot remove `new_to_old_crd.f': No such file or directory
/bin/rm: cannot remove `fix_new_inpcrd_vel.f': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm: cannot remove `*.o': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.mod
/bin/rm: cannot remove `*.mod': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/build_amoeba'
cd netcdf/src; make clean
make[1]: Entering directory `/usr/local/amber9/src/netcdf/src'
Makefile:4: macros.make: No such file or directory
rules.make:118: warning: overriding commands for target `/'
Makefile:173: warning: ignoring old commands for target `/'
rules.make:120: warning: overriding commands for target `/'
rules.make:118: warning: ignoring old commands for target `/'
rules.make:122: warning: overriding commands for target `/'
rules.make:120: warning: ignoring old commands for target `/'
rules.make:124: warning: overriding commands for target `/'
rules.make:122: warning: ignoring old commands for target `/'
rules.make:127: warning: overriding commands for target `/'
rules.make:124: warning: ignoring old commands for target `/'
rules.make:130: warning: overriding commands for target `/'
rules.make:127: warning: ignoring old commands for target `/'
rules.make:145: warning: overriding commands for target `/man1'
rules.make:142: warning: ignoring old commands for target `/man1'
rules.make:147: warning: overriding commands for target `/man3'
rules.make:142: warning: ignoring old commands for target `/man3'
rules.make:150: warning: overriding commands for target `/man3f'
rules.make:142: warning: ignoring old commands for target `/man3f'
rules.make:154: warning: overriding commands for target `/man3f90'
rules.make:142: warning: ignoring old commands for target `/man3f90'
make[1]: *** No rule to make target `macros.make'. Stop.
make[1]: Leaving directory `/usr/local/amber9/src/netcdf/src'
make: [clean] Error 2 (ignored)
cd netcdf/lib && rm -f libnetcdf.a
/bin/sh: line 0: cd: netcdf/lib: No such file or directory
make: [clean] Error 1 (ignored)
cd netcdf/include && rm -f *.mod
/bin/sh: line 0: cd: netcdf/include: No such file or directory
make: [clean] Error 1 (ignored)

=============================================================
These errors are unclear to me.

*$make parallel*

ERRORS======================================================

g95 -c -O3 -fno-second-underscore -march=nocona -o zung2r.o _zung2r.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dlapy3.f > _dlapy3.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dlapy3.o _dlapy3.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zladiv.f > _zladiv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zladiv.o _zladiv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zlarf.f > _zlarf.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zlarf.o _zlarf.f
ar rv lapack.a dsyev.o dsygv.o dlansy.o dsytrd.o dorgtr.o dsteqr.o dsterf.o
dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o dsytd2.o dlatrd.o dorgql.o
dorgqr.o dlasrt.o dlaset.o dlanst.o dlaev2.o dlasr.o dlapy2.o dlartg.o
dlae2.o dorg2r.o dlarft.o dlarfb.o dorg2l.o dlarfg.o dlarf.o dspev.o
dlansp.o dsptrd.o dopgtr.o dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o
dpptrs.o dpptrf.o dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o
dgebal.o dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o
dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o
dspevd.o dstedc.o dopmtr.o dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o
dlaed9.o dlamrg.o dlaed2.o dlaed3.o dpotrf.o dsygst.o dpotf2.o dsygs2.o
dlaebz.o dlagtf.o dlagts.o dormqr.o dormql.o dorm2l.o dlaed4.o dlaed5.o
dlaed6.o ieeeck.o dsyevx.o dsyevd.o dstebz.o dstein.o dormtr.o zheev.o
lsame.o zlanhe.o zlascl.o zhetrd.o zungtr.o zsteqr.o zlassq.o zlatrd.o
zhetd2.o zungql.o zungqr.o zlasr.o zlaset.o zlacgv.o zlarfg.o zung2l.o
zlarft.o zlarfb.o zung2r.o dlapy3.o zladiv.o zlarf.o
ar: creating lapack.a
a - dsyev.o
a - dsygv.o
a - dlansy.o
a - dsytrd.o
a - dorgtr.o
a - dsteqr.o
a - dsterf.o
a - dlascl.o
a - dlamch.o
a - xerbla.o
a - ilaenv.o
a - dlassq.o
a - dsytd2.o
a - dlatrd.o
a - dorgql.o
a - dorgqr.o
a - dlasrt.o
a - dlaset.o
a - dlanst.o
a - dlaev2.o
a - dlasr.o
a - dlapy2.o
a - dlartg.o
a - dlae2.o
a - dorg2r.o
a - dlarft.o
a - dlarfb.o
a - dorg2l.o
a - dlarfg.o
a - dlarf.o
a - dspev.o
a - dlansp.o
a - dsptrd.o
a - dopgtr.o
a - dppsv.o
a - dspsv.o
a - dgeev.o
a - dsptrs.o
a - dsptrf.o
a - dpptrs.o
a - dpptrf.o
a - dgebak.o
a - dtrevc.o
a - dlacpy.o
a - dhseqr.o
a - dorghr.o
a - dgehrd.o
a - dgebal.o
a - dlange.o
a - dlabad.o
a - dlahqr.o
a - dlarfx.o
a - dlanhs.o
a - dlaln2.o
a - dgehd2.o
a - dlahrd.o
a - dlanv2.o
a - dladiv.o
a - dgerq2.o
a - dorm2r.o
a - dlarnv.o
a - dgeqr2.o
a - dlaruv.o
a - dspevd.o
a - dstedc.o
a - dopmtr.o
a - dlaed0.o
a - dlaed1.o
a - dlaed7.o
a - dlaeda.o
a - dlaed8.o
a - dlaed9.o
a - dlamrg.o
a - dlaed2.o
a - dlaed3.o
a - dpotrf.o
a - dsygst.o
a - dpotf2.o
a - dsygs2.o
a - dlaebz.o
a - dlagtf.o
a - dlagts.o
a - dormqr.o
a - dormql.o
a - dorm2l.o
a - dlaed4.o
a - dlaed5.o
a - dlaed6.o
a - ieeeck.o
a - dsyevx.o
a - dsyevd.o
a - dstebz.o
a - dstein.o
a - dormtr.o
a - zheev.o
a - lsame.o
a - zlanhe.o
a - zlascl.o
a - zhetrd.o
a - zungtr.o
a - zsteqr.o
a - zlassq.o
a - zlatrd.o
a - zhetd2.o
a - zungql.o
a - zungqr.o
a - zlasr.o
a - zlaset.o
a - zlacgv.o
a - zlarfg.o
a - zung2l.o
a - zlarft.o
a - zlarfb.o
a - zung2r.o
a - dlapy3.o
a - zladiv.o
a - zlarf.o
ranlib lapack.a
make[2]: Leaving directory `/usr/local/amber9/src/lapack'
cd ../blas; make
make[2]: Entering directory `/usr/local/amber9/src/blas'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dasum.f > _dasum.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dasum.o _dasum.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp daxpy.f > _daxpy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o daxpy.o _daxpy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dcabs1.f > _dcabs1.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dcabs1.o _dcabs1.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dcopy.f > _dcopy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dcopy.o _dcopy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ddot.f > _ddot.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ddot.o _ddot.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dgbmv.f > _dgbmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dgbmv.o _dgbmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dgemm.f > _dgemm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dgemm.o _dgemm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dgemv.f > _dgemv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dgemv.o _dgemv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dger.f > _dger.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dger.o _dger.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dnrm2.f > _dnrm2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dnrm2.o _dnrm2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp drot.f > _drot.f
g95 -c -O3 -fno-second-underscore -march=nocona -o drot.o _drot.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp drotg.f > _drotg.f
g95 -c -O3 -fno-second-underscore -march=nocona -o drotg.o _drotg.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsbmv.f > _dsbmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsbmv.o _dsbmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dscal.f > _dscal.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dscal.o _dscal.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dspmv.f > _dspmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dspmv.o _dspmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dspr.f > _dspr.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dspr.o _dspr.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dspr2.f > _dspr2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dspr2.o _dspr2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dswap.f > _dswap.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dswap.o _dswap.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsymm.f > _dsymm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsymm.o _dsymm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsymv.f > _dsymv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsymv.o _dsymv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsyr.f > _dsyr.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsyr.o _dsyr.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsyr2.f > _dsyr2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsyr2.o _dsyr2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsyr2k.f > _dsyr2k.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsyr2k.o _dsyr2k.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dsyrk.f > _dsyrk.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dsyrk.o _dsyrk.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtbmv.f > _dtbmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtbmv.o _dtbmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtbsv.f > _dtbsv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtbsv.o _dtbsv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtpmv.f > _dtpmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtpmv.o _dtpmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtpsv.f > _dtpsv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtpsv.o _dtpsv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtrmm.f > _dtrmm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtrmm.o _dtrmm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtrmv.f > _dtrmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtrmv.o _dtrmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtrsm.f > _dtrsm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtrsm.o _dtrsm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dtrsv.f > _dtrsv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dtrsv.o _dtrsv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dummy.f > _dummy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dummy.o _dummy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dzasum.f > _dzasum.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dzasum.o _dzasum.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp dznrm2.f > _dznrm2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o dznrm2.o _dznrm2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp idamax.f > _idamax.f
g95 -c -O3 -fno-second-underscore -march=nocona -o idamax.o _idamax.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp isamax.f > _isamax.f
g95 -c -O3 -fno-second-underscore -march=nocona -o isamax.o _isamax.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp lsame.f > _lsame.f
g95 -c -O3 -fno-second-underscore -march=nocona -o lsame.o _lsame.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp scopy.f > _scopy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o scopy.o _scopy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sswap.f > _sswap.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sswap.o _sswap.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sscal.f > _sscal.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sscal.o _sscal.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sasum.f > _sasum.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sasum.o _sasum.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp snrm2.f > _snrm2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o snrm2.o _snrm2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sdot.f > _sdot.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sdot.o _sdot.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ssyr2k.f > _ssyr2k.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ssyr2k.o _ssyr2k.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp saxpy.f > _saxpy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o saxpy.o _saxpy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sgemv.f > _sgemv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sgemv.o _sgemv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ssyr2.f > _ssyr2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ssyr2.o _ssyr2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ssymv.f > _ssymv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ssymv.o _ssymv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sgemm.f > _sgemm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sgemm.o _sgemm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp strmm.f > _strmm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o strmm.o _strmm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp strmv.f > _strmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o strmv.o _strmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp sger.f > _sger.f
g95 -c -O3 -fno-second-underscore -march=nocona -o sger.o _sger.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zher2k.f > _zher2k.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zher2k.o _zher2k.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zswap.f > _zswap.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zswap.o _zswap.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zgemv.f > _zgemv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zgemv.o _zgemv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zhemv.f > _zhemv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zhemv.o _zhemv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zscal.f > _zscal.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zscal.o _zscal.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zdotc.f > _zdotc.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zdotc.o _zdotc.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zaxpy.f > _zaxpy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zaxpy.o _zaxpy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zher2.f > _zher2.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zher2.o _zher2.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zdscal.f > _zdscal.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zdscal.o _zdscal.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ztrmv.f > _ztrmv.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ztrmv.o _ztrmv.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zcopy.f > _zcopy.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zcopy.o _zcopy.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp ztrmm.f > _ztrmm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o ztrmm.o _ztrmm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zgemm.f > _zgemm.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zgemm.o _zgemm.f
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp zgerc.f > _zgerc.f
g95 -c -O3 -fno-second-underscore -march=nocona -o zgerc.o _zgerc.f
ar rv blas.a dasum.o daxpy.o dcabs1.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o
dger.o dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o
dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o
dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o
isamax.o lsame.o scopy.o sswap.o sscal.o sasum.o snrm2.o sdot.o ssyr2k.o
saxpy.o sgemv.o ssyr2.o ssymv.o sgemm.o strmm.o strmv.o sger.o zher2k.o
zswap.o zgemv.o zhemv.o zscal.o zdotc.o zaxpy.o zher2.o zdscal.o ztrmv.o
zcopy.o ztrmm.o zgemm.o zgerc.o
ar: creating blas.a
a - dasum.o
a - daxpy.o
a - dcabs1.o
a - dcopy.o
a - ddot.o
a - dgbmv.o
a - dgemm.o
a - dgemv.o
a - dger.o
a - dnrm2.o
a - drot.o
a - drotg.o
a - dsbmv.o
a - dscal.o
a - dspmv.o
a - dspr.o
a - dspr2.o
a - dswap.o
a - dsymm.o
a - dsymv.o
a - dsyr.o
a - dsyr2.o
a - dsyr2k.o
a - dsyrk.o
a - dtbmv.o
a - dtbsv.o
a - dtpmv.o
a - dtpsv.o
a - dtrmm.o
a - dtrmv.o
a - dtrsm.o
a - dtrsv.o
a - dummy.o
a - dzasum.o
a - dznrm2.o
a - idamax.o
a - isamax.o
a - lsame.o
a - scopy.o
a - sswap.o
a - sscal.o
a - sasum.o
a - snrm2.o
a - sdot.o
a - ssyr2k.o
a - saxpy.o
a - sgemv.o
a - ssyr2.o
a - ssymv.o
a - sgemm.o
a - strmm.o
a - strmv.o
a - sger.o
a - zher2k.o
a - zswap.o
a - zgemv.o
a - zhemv.o
a - zscal.o
a - zdotc.o
a - zaxpy.o
a - zher2.o
a - zdscal.o
a - ztrmv.o
a - zcopy.o
a - ztrmm.o
a - zgemm.o
a - zgerc.o
ranlib blas.a
make[2]: Leaving directory `/usr/local/amber9/src/blas'
cd ../lmod; make
make[2]: Entering directory `/usr/local/amber9/src/lmod'
cd xmin; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp xmin.f > _xmin.f
g95 -c -O3 -fno-second-underscore -march=nocona -o xmin.o _xmin.f
make[3]: Leaving directory `/usr/local/amber9/src/lmod/xmin'
cd lmod; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/usr/local/mpich2-1.0.7-g95//include -P -DMPI
-xassembler-with-cpp lmod.f > _lmod.f
g95 -c -O3 -fno-second-underscore -march=nocona -o lmod.o _lmod.f
make[3]: Leaving directory `/usr/local/amber9/src/lmod/lmod'
ar rv lmod.a xmin/*.o lmod/*.o
ar: creating lmod.a
a - xmin/xmin.o
a - lmod/lmod.o
ranlib lmod.a
make[2]: Leaving directory `/usr/local/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
g95 -static -ffree-form -o sander.MPI evb_vars.o evb_input.o evb_init.o
evb_alloc.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o exchange_CM.o
evb_mcp.o evb_force.o diabatic.o evb_2stdebug.o egap_umb_2stdebug.o
exchange_gauss.o exchange_warshel.o morsify.o morse_anal2num.o evb_matrix.o
evb_ntrfc.o out_evb.o constants.o stack.o qmmm_module.o trace.o lmod.o
decomp.o icosasurf.o egb.o findmask.o pb_force.o pb_exmol.o pb_mpfrc.o
pb_direct.o pb_list.o np_force.o sa_driver.o relax_mat.o nmr.o multisander.o
sander.o trajene.o cshf.o nmrcal.o pearsn.o printe.o runmin.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 is_init.o constantph.o prn_dipoles.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 spatial_recip.o spatial_fft.o parms.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_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_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
qm2_dftb_module.o qm2_dftb_broyden.o qm2_dftb_dispersion_egr.o
qm2_dftb_dispersion_params.o qm2_dftb_dispersionread.o qm2_dftb_eglcao.o
qm2_dftb_energy.o qm2_dftb_ewevge.o qm2_dftb_externalchgrad.o
qm2_dftb_externalshift.o qm2_dftb_fermi.o qm2_dftb_forces.o qm2_dftb_gamma.o
qm2_dftb_gammamat.o qm2_dftb_get_qmmm_forces.o qm2_dftb_gettab.o
qm2_dftb_load_params.o qm2_dftb_long_range.o qm2_dftb_main.o
qm2_dftb_my_gradient.o qm2_dftb_my_mulliken.o qm2_dftb_repulsiv.o
qm2_dftb_self.o qm2_dftb_shift.o qm2_dftb_short_range.o qm2_dftb_skpar.o
qm2_dftb_slkode.o qm2_dftb_slktrafo.o \
                   qm_div.o force.o \
        ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/usr/local/mpich2-1.0.7-g95//lib
-lmpichf90 -lmpichf90 -lmpich -lpthread
/usr/local/mpich2-1.0.7-g95//lib/libmpich.a(ch3u_getinterfaces.o)(.text+0x87):
In function `MPIDU_CH3U_GetSockInterfaceAddr':
: warning: Using 'gethostbyname' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
evb_init.o(.data+0x460): undefined reference to `mpi_conversion_fn_null_'
evb_io.o(.data+0x458): undefined reference to `mpi_conversion_fn_null_'
qmmm_module.o(.data+0x448): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x450): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x2558): undefined reference to `mpi_conversion_fn_null_'
multisander.o(.data+0x458): more undefined references to
`mpi_conversion_fn_null_' follow
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2

==============================================================
The last portion of errors show some MPI routines not find. I think it is
MPI related problem. Awaiting for your early reply.

Thanks and regards
sudipta

On Sat, May 3, 2008 at 3:03 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> export PATH=/usr/local/mpich2-1.0.7-g95/bin/
>
> --->
>
> export PATH=/usr/local/mpich2-1.0.7-g95/bin/:$PATH
>
> Sorry about that - busy day....
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Ross Walker
> > Sent: Friday, May 02, 2008 2:19 PM
> > To: amber_at_scripps.edu
> > Subject: RE: AMBER: Installation problem of AMBER on cluster
> >
> > Hi Sudipta
> >
> > Did you replace the contents of ~/.bashrc with those two exports?
> >
> > You need to append these to your ~/.bashrc file. It should look
> something
> > like:
> >
> > # .bashrc
> > # User specific aliases and functions
> > # Source global definitions
> > if [ -f /etc/bashrc ]; then
> > . /etc/bashrc
> > fi
> > #default create 0700
> > umask 077
> > #CVS Specs
> > export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
> > export PATH=/usr/local/mpich2-1.0.7-g95/bin/
> >
> > I suggest though that you find someone else who has a username on the
> > machine and see what their default .bashrc file looks like. Do you have
> a
> > system administrator? Someone who set the machine up for you?
> >
> > Ross
> >
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of
> > sudipta sinha
> > Sent: Friday, May 02, 2008 1:30 PM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Installation problem of AMBER on cluster
> >
> > HIi Ross,
> >
> > After setting the two environment varible in .bashrc file and compiling
> > it
> > by source command
> > no command is working on the terminal(such as vi, scp, cp, mv etc.
> etc.).
> > I
> > don't understand what I will do. Please tell me.
> >
> > $vi .bashrc
> > export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
> > export PATH=/usr/local/mpich2-1.0.7-g95/bin/
> > $source .bashrc
> >
> > Thank and regards
> > sudipta
> >
> >
> > On Sat, May 3, 2008 at 12:37 AM, Ross Walker <ross_at_rosswalker.co.uk>
> > wrote:
> > Hi Sudipta
> >
> > This is from the log file:
> >
> > configure:3475: gcc -static -all-static conftest.c >&5
> > cc1: error: unrecognized command line option "-all-static"
> >
> > So that is the problem - thus try changing the export
> LDFLAGS=-all-static
> > to
> > just -static and try again.
> >
> > Good luck
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > be read every day, and should not be used for urgent or sensitive
> issues.
> >
> >
> >
> >
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of
> > sudipta sinha
> > Sent: Friday, May 02, 2008 11:30 AM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Installation problem of AMBER on cluster
> >
> > Hi Ross,
> >
> > Still I am getting some error during compilation of MPICH2.
> Here
> > the issue is coming from c compiler. Now I clearly tell you what I have
> > done.
> > In .bashrc file we put the commands
> > export FC=g95
> > export F90=g95
> > export LDFLAGS=-all-static
> > export FFLAGS=-static
> > export CFLAGS=-static
> > export CXXFLAGS=-static
> > export CXXLDFLAGS=-static
> > and then compiled it by $source .bashrc
> > Then I untar the file mpich2-1.0.7.tar.gz in /usr/local and also make
> a
> > directory mpich2-1.0.7-g95 in /usr/local. Then I have typed the
> > command
> > $./configure –prefix=/usr/local/mpich2-1.0.7-g95
> > But it is giving some errors
> > ERRORS:==================================================
> > Configuring MPICH2 version 1.0.7 with
> > '--prefix=/usr/local/mpich2-1.0.7-g95/' 'CFLAGS=-static' 'CXXFLAGS=-
> > static'
> > 'F90=g95' 'FFLAGS=-static' 'LDFLAGS=-all-static'
> > Running on system: Linux node3 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44
> > EST
> > 2007 x86_64 x86_64 x86_64 GNU/Linux
> > Executing mpich2prereq in /usr/local/mpich2-1.0.7/src/mpid/ch3 with
> > Executing mpich2prereq in /usr/local/mpich2-
> > 1.0.7/src/mpid/ch3/channels/sock
> > sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/mpich2prereq
> > sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/setup_pm
> > checking for gcc... gcc
> > checking for C compiler default output file name... configure: error: C
> > compiler cannot create executables
> > See `config.log' for more details.
> >
> >
> ==========================================================================
> > ==
> > =====
> >
> > I am also attaching the config.log file. Please see and tell me what is
> my
> > wrong.
> >
> > Thanks and regards
> > sudipta
> > On Fri, May 2, 2008 at 9:11 PM, Ross Walker <ross_at_rosswalker.co.uk>
> wrote:
> > Hi Sudipta,
> >
> > You should do the following if I remember correctly (assuming you are
> > using
> > the BASH shell):
> >
> > cd /usr/local
> > tar –xvzf mpich2-1.0.7.tar.gz
> > cd mpich2-1.0.7
> > export FC=g95
> > export F90=g95
> > export LDFLAGS=-all-static
> > export FFLAGS=-static
> > export CFLAGS=-static
> > export CXXFLAGS=-static
> > export CXXLDFLAGS=-static
> >
> > (note: you may not need the last 5 options, or they may not work, but it
> > is
> > useful to try since if you can build a static version it will help you
> > later
> > since you will not need to worry about setting all the library paths on
> > each
> > node etc.)
> >
> > ./configure –prefix=/usr/local/mpich2-1.0.7-g95
> >
> > make
> > make install
> >
> > (Then you can build the parallel version of AMBER – for amber 9)
> >
> > export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
> > export PATH=/usr/local/mpich2-1.0.7-g95/bin/
> >
> > (note: the two commands above should probably be put in the default
> bashrc
> > so they get set every time you login.)
> >
> > cd $AMBERHOME/src/
> > ./configure –static –mpich2 g95
> > make clean
> > make parallel
> >
> > Then you can run the parallel tests etc.
> >
> > Good luck,
> > Ross
> >
> >
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of
> > sudipta sinha
> > Sent: Friday, May 02, 2008 12:39 AM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Installation problem of AMBER on cluster
> >
> > Dear sir,
> >
> > can you please help me about the compilation procedure of
> > mpich2.
> > We have installed our mpich2 by the following commands.
> > cd /usr/local/
> > tar -zxvf mpich2-1.0.7.tar.gz
> > cd mpich2-1.0.7
> > ./configure
> > make
> > make install
> > Our operating system is RHEL4 and I think the default c and fortran
> > compiler in RHEL4 are used during the compilation. Here we didn't set
> g95
> > compiler for the compilation of mpich2. So, please guide me how to
> install
> > mpich2 with g95 and gcc (default c compiler in RHEL4) compiler.
> >
> > sudipta
> > On Fri, May 2, 2008 at 12:25 AM, David A. Case <case_at_scripps.edu> wrote:
> > On Thu, May 01, 2008, sudipta sinha wrote:
> > >
> > > make clean
> > >
> > make: *** [clean] Error 2
> >
> > So, "make clean" did not work, because there is no config.h file.
> > >
> > > ./configure -mpich2 g95
> >
> > This step creates the config.h file. So, you need to do "make clean"
> now,
> > (i.e. after the configure step).
> > >
> > > MPI_HOME is set to /usr/local/
> > This implies that the mpich2 libraries (like libmpichf90.*) are in
> > /usr/local/lib. Make sure that is the case.
> >
> > > evb_init.o(.data+0x460): undefined reference to
> > `mpi_conversion_fn_null_'
> > It seems to have found the libraries. The most common problem here is
> > that
> > the mpich2 libraries were compiled with a different fortran compiler
> than
> > g95.
> > Is that the case?
> >
> > ...good luck...dac
> >
> > -----------------------------------------------------------------------
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> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
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> >
> >
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>
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