[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin

Gerrit Groenhof Mon, 15 Dec 2008 03:45:53 -0800

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Today's Topics:

   1. RE: Subject: Re: Re: [gmx-users] Gromacs 4 bug? (Berk Hess)
   2. Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7       QM/MM
      (Laercio Pol Fachin)


How was the mopac library compiled? You might have to link also to -lg2c?

Gerrit

Message: 2
Date: Mon, 15 Dec 2008 03:40:53 -0800 (PST)
From: Laercio Pol Fachin <laercio...@yahoo.com.br>
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
        MOPAC7  QM/MM
To: gmx-users@gromacs.org
Message-ID: <627734.45704...@web51508.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi!

Now, I tried to configure Mopac QMMM not manually, that is:

"./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac 
LDFLAGS=-L/usr/local/mopac7-1.10/src"

It ran O.K., but I had other problem now:

---

ranlib .libs/libgmxpreprocess_mpi.a
creating libgmxpreprocess_mpi.la
(cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la 
libgmxpreprocess_mpi.la)
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -DUSE_MOPACÂ  -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o 
-MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c
mv -f .deps/grompp.Tpo .deps/grompp.Po
/bin/sh ../../libtool --tag=CCÂ Â  --mode=link mpiccÂ  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loopsÂ  
-L/usr/local/mopac7-1.10/srcÂ Â  -o grompp grompp.o libgmxpreprocess_mpi.la 
../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.laÂ  -lxml2Â  -lnsl -lfftw3f -lm 
-lmopacÂ  -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -o grompp grompp.oÂ  -L/usr/local/mopac7-1.10/src 
./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a 
../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz -lnsl -lfftw3f -lm -lmopac 
/usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so /usr/lib/libxcb-xlib.so 
/usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so -ldl
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x160): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x21f): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x296): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x2d0): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
(.text+0x8b2): undefined reference to `__ctype_b'
/usr/local/mopac7-1.10/src/libmopac.a(lread.o):(.text+0xb05): more undefined 
references to `__ctype_b' follow
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1

---

I tried it with both Gromacs 4.0.2 and 3.3.3, and the same output error 
appears; so, probably, it's something I forgot... Any idea?

LaÃ©rcio


Message: 4
Date: Fri, 12 Dec 2008 10:18:20 +0100
From: Gerrit Groenhof <ggro...@gwdg.de>
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with,
        MOPAC7 QM/MM
To: gmx-users@gromacs.org
Message-ID: <49422c5c.2060...@gwdg.de>
Content-Type: text/plain; charset=windows-1252; format=flowed

Ok, but somehow these flags do not show up in the compilation output(bit messy copy/paste):

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused

-funroll-all-loops -o grompp grompp.oÃƒâ€š  ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl

There should be a -lmopac somewhere then.

Try a make distclean, and reconfigure with the LIBS and LDFLAGS set.

GErrit

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

Message: 4
Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST)
From: Laercio Pol Fachin <laercio...@yahoo.com.br>
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
        MOPAC7 QM/MM
To: gmx-users@gromacs.org
Message-ID: <554128.85516...@web51510.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Well...

The LDFLAGS and LIBS I have set manually:

LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a
LIBS = -lxml2Ã‚  -lnsl -lfftw3f -lmopac -lmÃ‚ Ã‚  -lSM -lICE -lX11

Probably, I might have confused the correct "gmxmop.f" and

"dcart.f" place: should them stay in the MOPAC folder with files and
objects (mopac7-1.10/src) or in LINUX folder with library files
(usr/local/lib/)?

LaÃƒÂ©rcio
Message: 2
Date: Thu, 11 Dec 2008 14:51:34 +0100
From: Gerrit Groenhof <ggro...@gwdg.de>
Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
        MOPAC7 QM/MM, (Laercio Pol Fachin)
To: gmx-users@gromacs.org
Message-ID: <49411ae6.6020...@gwdg.de>
Content-Type: text/plain; charset=windows-1252; format=flowed

Today's Topics:


Well, I removed that line, and "make" gone further, but I

stopped in other error:

---
make[3]: Entrando no diretÃƒÆ’Ã‚Â³rio

`/usr/local/gromacs-4.0.2/src/kernel'

/bin/sh ../../libtool --tag=CCÃƒâ€š Ãƒâ€š  --mode=link mpiccÃƒâ€š  -O3

-fomit-frame-pointer -finline-functions -Wall -Wno-unused

-funroll-all-loopsÃƒâ€š

Ãƒâ€š  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
../gmxlib/libgmx_mpi.laÃƒâ€š -lxml2Ãƒâ€š -lnsl -lfftw3f -lmÃƒâ€š Ãƒâ€š

-lSM -lICE -lX11

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused

-funroll-all-loops -o grompp grompp.oÃƒâ€š  ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a

/usr/lib/libxml2.so -lz

-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl

../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function

`call_mopac_SH':

qm_mopac.c:(.text+0x286): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretÃƒÆ’Ã‚Â³rio

`/usr/local/gromacs-4.0.2/src/kernel'

make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretÃƒÆ’Ã‚Â³rio `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretÃƒÆ’Ã‚Â³rio `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1
---

Is there something I should do (better, I forgot to do)?

Did you use the gromacs adapted mopac sources? If not, please retreivethem from the website (below).

Alternatively, you seem to have forgotten to set the LIBS to -lmopac andLDFLAGS to the location of the mopac library.


Gerrit

Thanks in advance,
LaÃƒÆ’Ã‚Â©rcio



Message: 2
Date: Tue, 09 Dec 2008 12:26:57 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
        MOPAC7 QM/MM
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <493dc961.4000...@anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed

Laercio Pol Fachin wrote:

Dear GMX users:

I'm facing problems installing Gromacs 4.0.2 with mopac7

QM/MM.

I have downloaded MOPAC7 for SourceForge, as linked in previous

mails,

and installed it. After, MPICH and fftw 3.0.1. So:

"./configure

--enable-mpi --with-qmmm-mopac" runs O.K., but, during

"make":

(some shell indications in Portuguese):
---
make[3]: Entrando no diretÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â³rio

`/usr/local/gromacs-4.0.2/src/mdlib'

/bin/sh ../../libtool --tag=CC   --mode=compile mpicc

-DHAVE_CONFIG_H

-I. -I../../src -I/usr/include/libxml2 -I../../include-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"

-O3

-fomit-frame-pointer

-finline-functions -Wall-Wno-unused -funroll-all-loops -MT

qm_mopac.lo

-MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2-I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused-funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo

-c

qm_mopac.c -o qm_mopac.o
qm_mopac.c:52:17: error: nsb.h: Arquivo ou

diretÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â³rio nÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â£o

encontrado
My Portuguese is not so hot, but I figure this error translates as"nsb.h: File or directory not found". That means what it

says.

GROMACSversion 3.3.x had this file, version 4.x doesn't. I had a look atqm_mopac.c and I don't think it was using any of the contents of
nsb.h,
so you should be safe to remove this line from qm_mopac.c. Do let usknow how you get on.
Mark
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http://br.maisbuscados.yahoo.com
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[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin

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