[gmx-users] Gromacs-3.3.1 installation

Wed Apr 26 10:18:52 CEST 2006

Hi

I now tried to install gromacs in a separate directory and not the source
tree which is:

/work1/r0914/gromacs/

I got following error while

Make
____________________________________________________________________________
cc -DHAVE_CONFIG_H -I. -I. -I../../../src -I/usr/X11R6/include
-I../../../include -I/users/ums/r0914/fftw-3.1.1/include -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops
-MT ilasrt2.lo -MD -MP -MF .deps/ilasrt2.Tpo -c ilasrt2.c -o ilasrt2.o
/bin/sh ../../../libtool --tag=CC --mode=link cc  -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops
-L/users/ums/r0914/fftw-3.1.1/lib   -o liblapack.la   dbdsdc.lo dgetf2.lo
dlamrg.lo dlarnv.lo dlasd0.lo dlasda.lo dlasq6.lo dorgl2.lo dormqr.lo
dbdsqr.lo dgetrf.lo dlange.lo dlasd1.lo dtrtri.lo dlasdq.lo dlasr.lo
dorglq.lo dormtr.lo dgebd2.lo dlabrd.lo dlanst.lo dlasd2.lo dlasdt.lo
dlasrt.lo dorgqr.lo dstebz.lo dgebrd.lo dsytrd.lo dlacpy.lo dlapy2.lo
dlasd3.lo dlaset.lo dlassq.lo dorm2l.lo dgetrs.lo dstegr.lo dgelq2.lo
dlae2.lo dlasd4.lo dlasq1.lo dtrti2.lo dgetri.lo dlasv2.lo dorm2r.lo
dstein.lo dgelqf.lo dlaebz.lo dlarf.lo dlartg.lo dlasd5.lo dlasq2.lo
dlaswp.lo dormbr.lo dsterf.lo dgeqr2.lo dlaed6.lo dlarfb.lo dlaruv.lo
dlasd6.lo dlasq3.lo dlatrd.lo dorml2.lo dstevr.lo dgeqrf.lo dlagtf.lo
dlarfg.lo dlas2.lo dlasd7.lo dlasq4.lo dorg2r.lo dormlq.lo dsytd2.lo
dgesdd.lo dlagts.lo dlarft.lo dlascl.lo dlasd8.lo dlasq5.lo dorgbr.lo
dormql.lo dlaev2.lo dsteqr.lo dsyevr.lo dlasrt2.lo dlansy.lo dlar1vx.lo
dlarrbx.lo dlarrex.lo dlarrfx.lo dlarrvx.lo sbdsdc.lo sgetf2.lo slamrg.lo
slarnv.lo slasd0.lo slasda.lo slasq6.lo sorgl2.lo sormqr.lo sbdsqr.lo
sgetrf.lo slange.lo slasd1.lo ssytrd.lo slasdq.lo slasr.lo sorglq.lo
sormtr.lo sgebd2.lo slabrd.lo slanst.lo slasd2.lo slasdt.lo slasrt.lo
sorgqr.lo sstebz.lo sgebrd.lo sgetrs.lo slacpy.lo slapy2.lo slasd3.lo
slaset.lo slassq.lo sorm2l.lo sgetri.lo sstegr.lo sgelq2.lo slae2.lo
slasd4.lo slasq1.lo strti2.lo strtri.lo slasv2.lo sorm2r.lo sstein.lo
sgelqf.lo slaebz.lo slarf.lo slartg.lo slasd5.lo slasq2.lo slaswp.lo
sormbr.lo ssterf.lo sgeqr2.lo slaed6.lo slarfb.lo slaruv.lo slasd6.lo
slasq3.lo slatrd.lo sorml2.lo sstevr.lo sgeqrf.lo slagtf.lo slarfg.lo
slas2.lo slasd7.lo slasq4.lo sorg2r.lo sormlq.lo ssytd2.lo sgesdd.lo
slagts.lo slarft.lo slascl.lo slasd8.lo slasq5.lo sorgbr.lo sormql.lo
slaev2.lo ssteqr.lo ssyevr.lo slasrt2.lo slansy.lo slar1vx.lo slarrbx.lo
slarrex.lo slarrfx.lo slarrvx.lo ilasrt2.lo  -L/usr/X11R6/lib -lnsl -lfftw3f
-lm   -lSM -lICE -lX11  
libtool: link: `slarft.lo' is not a valid libtool object
make[4]: *** [liblapack.la] Error 1
make[4]: Leaving directory
`/work1/r0914/gromacs-3.3.1/src/gmxlib/gmx_lapack'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/work1/r0914/gromacs-3.3.1/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/work1/r0914/gromacs-3.3.1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/work1/r0914/gromacs-3.3.1/src'
make: *** [all-recursive] Error 1
____________________________________________________________________________

Kindly Help

Akshay Patny

|-----Original Message-----
|From: Rene Meier [mailto:rene.meier at pharmazie.uni-halle.de]
|Sent: Wednesday, April 26, 2006 2:40 AM
|To: akshay17 at olemiss.edu; Discussion list for GROMACS users
|Subject: Re: [gmx-users] Gromacs-3.3.1 installation
|
|On Wed, 26 Apr 2006 02:27:45 -0500
|Akshay Patny <akshay17 at olemiss.edu> wrote:
|
|> Hi
|>
|>
|>
|> I am trying to install Gromacs-3.3.1 The machine is SGI Altix and the
|output
|> of the uname -a for machine is:
|>
|>
|>
|> Linux redwood 2.6.5-7.244-sn2 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ia64
|ia64
|> ia64 GNU/Linux
|>
|>
|>
|> I do not have root privileges and I am trying to install it in the local
|> directory I have permissions for which is:
|>
|>
|>
|> I unpacked gromacs-3.3.1.tar in the /work1/r0914
|>
|>
|>
|> It made a directory /work1/r0914/gromacs-3.3.1/
|>
|>
|>
|> I first installed fftw-3.1.1 (both single precision and double precision
|> using) in a separate directory which is:
|>
|>
|>
|> ums/ro914/fftw-3.1.1
|>
|>
|>
|> Then, I cd to /work1/r0914/gromacs-3.3.1/
|>
|>
|>
|> # setenv CPPFLAGS -I/ ums/ro914/fftw-3.1.1/include
|>
|> # setenv LDFLAGS -L/ ums/ro914/fftw-3.1.1/lib
|>
|>
|>
|> # ./configure -prefix=/work1/r0914/gromacs-3.3.1/
|
|-prefix tells install to which directory it should copy the program and all
|of its files. I think it is not a good idea to install the program directly
|into the source tree. use something else as destination directory e.g
|/work1/r0914/prog.
|
|>
|>
|>
|> # make
|>
|>
|>
|> # make install
|>
|>
|>
|> I got the error in the make install which is:
|>
|>
|___________________________________________________________________________
|_
|> ______________
|>
|>
|>
|> /usr/bin/install: `./g_sham.1' and
|> `/work1/r0914/gromacs-3.3.1/man/man1/g_sham.1' are the same file
|>
|>  /usr/bin/install -c -m 644 './make_edi.1'
|> '/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1'
|>
|> /usr/bin/install: `./make_edi.1' and
|> `/work1/r0914/gromacs-3.3.1/man/man1/make_edi.1' are the same file
|>
|> make[3]: *** [install-man1] Error 1
|>
|> make[3]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1'
|>
|> make[2]: *** [install-am] Error 2
|>
|> make[2]: Leaving directory `/work1/r0914/gromacs-3.3.1/man/man1'
|>
|> make[1]: *** [install-recursive] Error 1
|>
|> make[1]: Leaving directory `/work1/r0914/gromacs-3.3.1/man'
|>
|> make: *** [install-recursive] Error 1
|>
|>
|___________________________________________________________________________
|_
|> ______________
|>
|>
|>
|> Let me know if you need other details
|>
|>
|>
|> Regards
|>
|> Akshay
|>
|>
|>
|> Akshay Patny
|>
|>
|>
|> Graduate Research Assistant
|> Faser Hall 417, Department of Medicinal Chemistry
|>
|> Research Institute of Pharmaceutical Sciences
|> University of Mississippi
|> University, MS 38677
|> E-mail: akshay17 at olemiss.edu
|> Tel: 662-915-1286 (office); Web: www.olemiss.edu
|>
|>
|>
|>
|
|
|--
|René Meier
|Institut für Pharmazeutische Chemie
|Martin-Luther-Universität Halle			email:
|	rene.meier at pharmazie.uni-halle.de
|Wolfgang-Langenbeck-Str. 4			phone:	(49)345 55-25043
|06120 Halle (Saale)				fax:	(49)345 55-27355
|Petition für ein Softwarepatent-Freies Europa:
|http://www.ffii.org/index.de.html
|