Monisha Hajra wrote:
Hi Justin,
I checked carefully. The make command also gave the same error as pasted
below. How should I deal this error?
For Windows systems, Gromacs needs to use internal XDR definitions (rather than
those that are available system-wide on most Unix/Linux machines). It appears
are not being properly defined. I have no experience with Windows machines, but
if you post the following information, perhaps someone can give you some pointers:
1. Your configuration command (and perhaps even the screen output would be
useful here, too)
2. Your config.h file (in the src subdirectory after configuration finishes)
-Justin
at' follow
.libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x35a6): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3785): undefined reference to `_xdr_int'
.libs/libxdrf.o:libxdrf.c:(.text+0x3a01): undefined reference to `_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xeb): undefined reference to
`_xdr_float
'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x126): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x161): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ec): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x22f): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x265): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x293): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2bf): undefined reference to
`_xdr_u_ch
ar'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x309): undefined reference to
`_xdr_u_sh
ort'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3c4): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3ed): undefined reference to
`_xdr_vect
or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x518): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x56c): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e1): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x60e): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x63b): undefined reference to
`_xdr_int'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x668): more undefined references
to `_xd
r_int' follow
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x764): undefined reference to
`_xdr_doub
le'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7bd): undefined reference to
`_xdr_floa
t'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7d4): undefined reference to
`_xdr_vect
or'
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x823): undefined reference to
`_xdr_stri
ng'
Creating library file: .libs/libgmx.dll.a
collect2: ld returned 1 exit status
make[4]: *** [libgmx.la <http://libgmx.la>] Error 1
make[4]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make: *** [all-recursive] Error 1
On Wed, Mar 30, 2011 at 1:54 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Monisha Hajra wrote:
Hi All,
I am installing GROMACS using cygwin.
I am following the steps as mentioned :
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO
*no 5, make install command give the following error in the end :*
What was your configuration command? Did "make" work properly?
It's odd that "make install" fails if "make" works. Do you have
proper permissions to install in this directory? Configuration and
compilation are done locally, but installation (if left at default
settings) is system-wide.
The actual error message is above what you have posted here.
ng'
Creating library file: .libs/libgmx.dll.a
collect2: ld returned 1 exit status
make[3]: *** [libgmx.la <http://libgmx.la> <http://libgmx.la>]
Error 1
make[3]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc/gmxlib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory
`/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
rc'
make: *** [install-recursive] Error 1
and* make links command gives the following error:*
*
Certainly "make links" will fail if the actual installation failed.
-Justin
*
*
$ make links
cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
(test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ;
exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or
directory
make: *** [links] Error 1
Can anyone de-code thsi error and help me how should I
successfully proceed for the same.
Thanks in advance.
Monisha *
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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