From: Adam Brenner (
Date: Tue Dec 18 2012 - 19:32:00 CST


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
[root_at_compute-1-2 vmd-1.9.1]# export VMDINSTALLNAME="vmd"
[root_at_compute-1-2 vmd-1.9.1]# export
[root_at_compute-1-2 vmd-1.9.1]# export

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*,
/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
University of California, Irvine