VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 18 2012 - 20:13:52 CST

Hi,
  What OS are you running on your cluster, specifically?
Also, please send the output of these commands:
uname -a
gcc --version
g++ --version

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 18, 2012 at 05:32:00PM -0800, Adam Brenner wrote:
> Howdy,
>
> I am trying to compile and install VMD on our HPC cluster from the source
> package and have ran into a snag, pasted below.
>
> We are using GCC 4.7.0 and 1.9.1 src package. My workflow as follows.
>
> [root_at_compute-1-2 vmd-1.9.1]# module load gcc/4.7.0
> [root_at_compute-1-2 vmd-1.9.1]# module list
> Currently Loaded Modulefiles:
> 1) gmp/5.0.2 2) mpc/0.9 3) mpfr/3.1.0 4)
> binutils/2.22 5) gcc/4.7.0
> [root_at_compute-1-2 vmd-1.9.1]# which gcc
> /data/apps/gcc-4.7.0/bin/gcc
> [root_at_compute-1-2 vmd-1.9.1]# export VMDINSTALLNAME="vmd"
> [root_at_compute-1-2 vmd-1.9.1]# export
> VMDINSTALLBINDIR="/data/apps/vmd/1.9.1/bin"
> [root_at_compute-1-2 vmd-1.9.1]# export
> VMDINSTALLLIBRARYDIR="/data/apps/vmd/1.9.1/lib"
>
> This ^^^ process sets up to use GCC 4.7.0 and using env. variables to
> define a custom path for our installation. Naturally I run ./configure in
> the vmd-1.9.1 and get prompted with I need to compile plugins first.
>
> [root_at_compute-1-2 vmd-1.9.1]# ./configure LINUXAMD64
>
> VMD plugin directory not found.
> Please compile the VMD plugins and do 'make distrib' to copy them
> into a 'plugins' directory linked or located in this directory.
> Be sure your PLUGINDIR environment variable is set before running
> 'make distrib' in the plugin build area.
>
> Halting configuration until VMD plugins are built.
> [root_at_compute-1-2 vmd-1.9.1]# cd ../plugins/
> [root_at_compute-1-2 plugins]# make LINUXAMD64
> TCLINC=/data/apps/tcl-8.5.5/include TCLLIB=/data/apps/tcl-8.5.5/lib
> Building Molecule File Reader plugins
> In file included from src/abinitplugin.c:65:0:
> src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined
> but not used [-Wunused-function]
> In file included from /usr/include/stdio.h:929:0,
> from src/biomoccaplugin.C:36:
> /usr/include/bits/stdio.h: In function '__ssize_t getline(char**, size_t*,
> FILE*)':
> /usr/include/bits/stdio.h:118:52: error: '__getdelim' was not declared in
> this scope
> make[2]: *** [../compile/lib_LINUXAMD64/molfile/biomoccaplugin.o] Error 1
> make[1]: *** [molfilelibs] Error 1
> make: *** [LINUXAMD64] Error 2
> [root_at_compute-1-2 plugins]#
>
> I cd into the plugins folder and run the make command and get the
> following error. This is the same error without or without the extra
> options (TCLINC/LIB) and different versions of GCC. 4.6.2, 4.6.3 and
> 4.7.0.
>
> Any hints or words of wisdom are much appreciated!
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> aebrenne_at_uci.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078