On 12/08/2011 7:48 AM, Park, Jae Hyun nmn wrote:
Dear GMX users,
Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3.
As a first test, when I run "make" in the directory of "template" I got the
following message:
------------------------------
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -I/usr/include/libxml2
-I/home/h1y/gromacs-4.5.3s/include -I/home/h1y/fftw3s/include -c -o work.o
work.c
cc -L/home/h1y/gromacs-4.5.3s/lib -L/home/h1y/fftw3s/lib -o work work.o -lmd
-lgmx -lfftw3f -lxml2 -lnsl -lm
/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x6): In function
`vmddlopen':
: undefined reference to `dlopen'
/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x11): In function
`vmddlerror':
: undefined reference to `dlerror'
/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x21): In function
`vmddlsym':
: undefined reference to `dlsym'
/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x31): In function
`vmddlclose':
: undefined reference to `dlclose'
collect2: ld returned 1 exit status
make: *** [work] Error 1
I would deeply appreciate if any help why I got those erros and how to figure
out.
Probably when the feature of using the VMD libraries was added, nobody
updated share/template/Makefile.am. You can either disable the use of
the DLOPEN facility from the VMD libraries (used for reading
non-GROMACS-native file formats) when you configure GROMACS, or you can
update share/template/Makefile.am so that
XLIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@
@GSL_LIBS@ @LIBS@
becomes
XLIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@
@GSL_LIBS@ @LIBS@ @DLOPEN_LIBS@
Then get the bootstrap script from a git install of GROMACS and run that
from the main source directory, before configure, make, make install.
Now the installed template Makefile should be able to link properly.
Mark
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