Eigenstate
Running into build problems trying to build for an IBM Power9 system
Before I dig too deep into this, I just wanted to know whether vmd-python was ever intended to run on Power systems...? If so, I will append the particular problem I'm seeing.
Oh boy... yes regular VMD will run on anything, including Power8. When making vmd-python I removed a lot of support for architectures I didn't feel comfortable supporting. Post your error and we can totally get it working!
First problem I ran into is that in /usr/include/gnu, the stubs.h file was trying to include stubs-32.h, but that file was not present. I installed everything I could think of, and couldn't get that fixed. So I just hacked stubs.h to point to the file which WAS present (stubs-64-v2.h).
Then, when I tried to do "python setup.py build" again, I got this:
[root@234bc51125a5 vmd-python]# python setup.py build running build running build_py package init file 'vmd/init.py' not found (or not a regular file) package init file 'vmd/init.py' not found (or not a regular file) Compiling VMD Finding libraries... LIB: libtcl8.5.so -> /lib64 INC: tcl.h -> /usr/include WARNING: Could not find library file 'libsqlite3.so' in standard library directories. Defaulting to: '/usr/lib/libsqlite3.so' LIB: libsqlite3.so -> /usr/lib
WARNING: Could not find include file 'sqlite3.h' in standard include directories. Defaulting to: '/usr/include/sqlite3.h' INC: sqlite3.h -> /usr/include/sqlite3.h LIB: libexpat.so -> /lib64 INC: expat.h -> /usr/include WARNING: Could not find library file 'libnetcdf.so' in standard library directories. Defaulting to: '/usr/lib/libnetcdf.so' LIB: libnetcdf.so -> /usr/lib
WARNING: Could not find include file 'netcdf.h' in standard include directories.
Defaulting to: '/usr/include/netcdf.h'
INC: netcdf.h -> /usr/include/netcdf.h
Building with:
CC: gcc
CXX: g++
CFLAGS: -I/usr/include
CXXFLAGS: -I/usr/include
LDFLAGS: -L/usr/lib64 -Wl,--no-as-needed,-rpath-link,/usr/lib64
Setting environment variables
Deleting previous plugin directory /vmd-1.9.3/vmd-python/build/lib/vmd/plugins
Compiling plugins to /vmd-1.9.3/vmd-python/build/lib/vmd/plugins
Building Molecule File Reader plugins
/usr/bin/ld: cannot find crti.o: No such file or directory
/usr/bin/ld: skipping incompatible /usr/lib/gcc/ppc64le-redhat-linux/4.8.5/libstdc++.so when searching for -lstdc++
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/ppc64le-redhat-linux/4.8.5/libgcc.a when searching for -lgcc
/usr/bin/ld: cannot find -lgcc
/usr/bin/ld: skipping incompatible /usr/lib/gcc/ppc64le-redhat-linux/4.8.5/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: cannot find -lgcc_s
/usr/bin/ld: skipping incompatible /usr/lib64/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib64/libc.a when searching for -lc
/usr/bin/ld: skipping incompatible //usr/lib64/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible //usr/lib64/libc.a when searching for -lc
/usr/bin/ld: cannot find -lc
/usr/bin/ld: skipping incompatible /usr/lib/gcc/ppc64le-redhat-linux/4.8.5/libgcc.a when searching for -lgcc
/usr/bin/ld: cannot find -lgcc
/usr/bin/ld: skipping incompatible /usr/lib/gcc/ppc64le-redhat-linux/4.8.5/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: cannot find -lgcc_s
/usr/bin/ld: cannot find crtn.o: No such file or directory
collect2: error: ld returned 1 exit status
make[2]: *** [abinitplugin.so] Error 1
make[1]: *** [molfilelibs] Error 1
make: *** [LINUX] Error 2
Traceback (most recent call last):
File "setup.py", line 377, in
I'll add a check for Power9 systems in setup.py and put the right logic back in the configure script which hopefully will fix your problems with plugins not building.
What's the output of:
python -c "import platform; print(platfom.system(), platform.machine()"?
You had some typos, but here's what I think you want:
$ python -c "import platform; print(platform.system(), platform.machine())" ('Linux', 'ppc64le') $
Just FYI, I would be very happy to act as an alpha test site, as you work to get this running on Power architectures. I will not be at all disappointed if this becomes an iterative process over several days.
Also, a question: I see that your implementation supports offscreen buffers (what I have come to know as "openglpbuffer"). My belief is that a prerequisite for painting to such pbuffers is the use of EGL in VMD, but I'm not sure that is true. In any case, does your VMD-as-a-Python-library have the option to use EGL?
Alright, I've made a new branch, ppc64le with an initial attempt. The build logic for this architecture seems to be pretty much identical except for no linkage to libstdc++ (hence the errors you were seeing earlier). Let me know if it works!
I am in the middle of polishing a new release and that does include support for offscreen rendering with EGL if you build with python setup.py build --egl but this is pretty experimental for now. You'll need the EGL development headers and (EGL/egl.h) and the OpenGL entry point library (libOpenGL.so) for the build to succeed.
So, I did these things:
git clone --branch ppc64le https://github.com/Eigenstate/vmd-python pip install --upgrade pip pip install --trusted-host pypi.python.orig numpy cd vmd-python python setup.py build
The last command generated this output:
[vmd-python]# python setup.py build running build running build_py package init file 'vmd/init.py' not found (or not a regular file) package init file 'vmd/init.py' not found (or not a regular file) Compiling VMD Finding libraries... LIB: libtcl8.5.so -> /usr/lib64/ INC: tcl.h -> /usr/include/ error: None [vmd-python]#
I will now attempt the "python setup.py install" and the next comment will contain those results.
heh.
"python setup.py install" gave me almost the exact same output as "python setup.py build":
[vmd-python]# python setup.py install running install running build running build_py package init file 'vmd/init.py' not found (or not a regular file) package init file 'vmd/init.py' not found (or not a regular file) Compiling VMD Finding libraries... LIB: libtcl8.5.so -> /usr/lib64/ INC: tcl.h -> /usr/include/ error: None [vmd-python]#
Maybe that missing init.py file is actually something important?
For future reference, can you point me to the EGL/egl.h and the libOpenGL.so?
Hmmmm, that's weird. It's not the init.py, that's a benign error as that file is moved from elsewhere during installation. Although the output is missing it probably is failing to find libsqlite3. I've committed some better error messages. What distro are you running?
On Debian, you'll need the following packages for the dependencies:
- libegl1-mesa-dev
- libopengl0
- libsqlite3-dev
- libnetcdf-dev
- libexpat1-dev
- tcl8.5-dev
Here's what I see when I type "cat /etc/os-release":
NAME="CentOS Linux" VERSION="7 (AltArch)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (AltArch)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7:server" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"
So, I tried on a simpler P9 system, with fewer bells and whistles, and it did give me more debug info:
[fossum@fstgbfen1 ~]$ git clone --branch ppc64le https://github.com/Eigenstate/vmd-python
Cloning into 'vmd-python'...
remote: Enumerating objects: 46, done.
remote: Counting objects: 100% (46/46), done.
remote: Compressing objects: 100% (32/32), done.
remote: Total 9038 (delta 25), reused 30 (delta 14), pack-reused 8992
Receiving objects: 100% (9038/9038), 39.11 MiB | 14.21 MiB/s, done.
Resolving deltas: 100% (3733/3733), done.
Checking out files: 100% (2498/2498), done.
[fossum@fstgbfen1 ~]$ cd vmd-python
[fossum@fstgbfen1 vmd-python]$ python setup.py build
running build
running build_py
package init file 'vmd/init.py' not found (or not a regular file)
package init file 'vmd/init.py' not found (or not a regular file)
Compiling VMD
Finding libraries...
LIB: libtcl8.5.so -> /usr/lib64/
INC: tcl.h -> /usr/include/
Traceback (most recent call last):
File "setup.py", line 407, in
On this system, when I type "cat /etc/os-release" I get this:
[fossum@fstgbfen1 vmd-python]$ cat /etc/os-release NAME="Red Hat Enterprise Linux Server" VERSION="7.5 (Maipo)" ID="rhel" ID_LIKE="fedora" VARIANT="Server" VARIANT_ID="server" VERSION_ID="7.5" PRETTY_NAME="Red Hat Enterprise Linux Server 7.5 (Maipo)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:redhat:enterprise_linux:7.5:GA:server" HOME_URL="https://www.redhat.com/" BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7" REDHAT_BUGZILLA_PRODUCT_VERSION=7.5 REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux" REDHAT_SUPPORT_PRODUCT_VERSION="7.5" [fossum@fstgbfen1 vmd-python]$
I searched for libsqlite3.so in my /usr directory, and it is not there. Should I be doing a 'yum install' of one or more of the following:
sqlite-devel.ppc64le : Development tools for the sqlite3 embeddable SQL database sqlite-doc.noarch : Documentation for sqlite sqlite-tcl.ppc64le : Tcl module for the sqlite3 embeddable SQL database engine sqlite2-devel.ppc64le : Development files for SQLite sqlite2-tcl.ppc64le : Tcl bindings for sqlite sqlite3-dbf.ppc64le : Converter of XBase / FoxPro tables to SQLite sqlite.ppc64le : Library that implements an embeddable SQL database engine sqlite2.ppc64le : Embeddable SQL engine in a C library
?
Progress! I noodled around and concluded that installing the following three libraries got me to a place where I'm actually doing non-trivial things in "python setup.py build":
yum install sqlite-devel.ppc64le yum install netcdf.ppc64le yum install netcdf-devel.ppc64le
"python setup.py build" finished. "python setup.py install" finished. I saved the text of both steps in files if you want to look them over in detail.
The last few lines of the install step looked like this:
byte-compiling /usr/lib/python2.7/site-packages/vmd/test/test_material.py to test_material.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/test/test_molecule.py to test_molecule.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/test/test_selection.py to test_selection.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/init.py to init.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/Molecule.py to Molecule.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/Label.py to Label.pyc byte-compiling /usr/lib/python2.7/site-packages/vmd/Material.py to Material.pyc running install_egg_info Writing /usr/lib/python2.7/site-packages/vmd_python-3.0.0-py2.7.egg-info
Does that look good?
I think that is normal. The best test is of course to write a short python script. Something like: import vmd in an interactive or batch python session should now work, and help vmd should too.
OK, so I started an interactive session, and this happened:
[root@f52816e1f650 vmd-1.9.3]# python Python 2.7.5 (default, Oct 30 2018, 23:44:29) [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import vmd Traceback (most recent call last): File "
", line 1, in File "/usr/lib/python2.7/site-packages/vmd/init.py", line 25, in vmd = imp.load_dynamic(name, vmdlib) ImportError: /usr/lib/python2.7/site-packages/vmd/libvmd.so: cannot dynamically load executable
And here's what's going on with that library:
[root@f52816e1f650 vmd-1.9.3]# ls -lt /usr/lib/python2.7/site-packages/vmd/*.so -rwxr-xr-x 1 root root 6198512 Feb 27 18:46 /usr/lib/python2.7/site-packages/vmd/libvmd.so [root@f52816e1f650 vmd-1.9.3]#
And (perhaps unsurprisingly) when I tried "help vmd" I got this:
[root@f52816e1f650 vmd-1.9.3]# python Python 2.7.5 (default, Oct 30 2018, 23:44:29) [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
help vmd File "
", line 1 help vmd ^ SyntaxError: invalid syntax
Ok, serves me right for not testing things. Shoulda been help(vmd), but that isn't the problem. I think the .so wasn't compiled as a dynamically loaded executable, since it was missing the PIC argument during compilation. I've got a pull request open. Does making those changes fix the problem?
I'm stupid about doing things with "git". Should I just do another git clone --branch ppc64le https://github.com/Eigenstate/vmd-python and then re-do the builds?
I'm going to take a break. I'll be back here around 7PM Central Time, and maybe the "git pull request" will be pulled into the main line, or whatever y'all do to synchronize these things, and I can do a fresh git clone?
Sure. You can already do a clone off of my fork, it just isn't in the mainline yet. git clone --branch ppc64le [email protected]:jvermaas/vmd-python.git
[root@f52816e1f650 vmd-1.9.3]# git clone --branch ppc64le [email protected]:jvermaas/vmd-python.git Cloning into 'vmd-python'... Permission denied (publickey). fatal: Could not read from remote repository.
Please make sure you have the correct access rights and the repository exists. [root@f52816e1f650 vmd-1.9.3]#
Weird. I assume the web version shows up fine? https://github.com/jvermaas/vmd-python I know I have my ssh keys setup, but it looks like above you use the https version instead, so that might be the issue.
Yes, thank you! I now am trying to build and install your version. More info soon.
I merged @jvermaas pull request so you can also try the ppc64le branch again
OK, so that's different...
I did the following with BOTH of your builds: (a) rm -rf vmd-python (b) git clone --branch ppc64le https://github.com/{name}/vmd-python (c) cd vmd-python (d) python setup.py build (e) python setup.py install (f) python (g) >>> import vmd
In both cases, the resulting errors were as follows:
Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/xsfplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/xsfplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pbeqplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pbeqplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/graspplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/graspplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dmsplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dmsplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/parmplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/parmplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/spiderplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/spiderplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/molemeshplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/molemeshplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dtrplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dtrplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/brixplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/brixplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/parm7plugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/parm7plugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/fs4plugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/fs4plugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/maeffplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/maeffplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/raster3dplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/raster3dplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/ccp4plugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/ccp4plugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/msmsplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/msmsplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/plyplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/plyplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pltplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pltplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/situsplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/situsplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/biomoccaplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/biomoccaplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/amiraplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/amiraplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/vtkplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/vtkplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/edmplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/edmplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/gromacsplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/gromacsplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/phiplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/phiplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/grdplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/grdplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pdbxplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/pdbxplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/avsplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/avsplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/mdfplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/mdfplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/cubeplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/cubeplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dsn6plugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dsn6plugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/gridplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/gridplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/mapplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/mapplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dxplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/dxplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/stlplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/stlplugin.so Warning) Unable to dlopen '/usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/uhbdplugin.so': Unable to dlopen plugin file /usr/lib/python2.7/site-packages/vmd/plugins/LINUXPPC64/molfile/uhbdplugin.so
I am but an egg, but I'm guessing the plugins need the same treatment you gave the main library?
PROGRESS! You can choose to ignore these errors, unless you happen to need to load a file that these plugins are there to handle. I suspect its the same sort of issue with -fPIC not getting called, since typically these get compiled into the executable in a stand-alone VMD build.
Well, when I try "help(vmd)" I get an error:
help(vmd) Traceback (most recent call last): File "
", line 1, in NameError: name 'vmd' is not defined