Running into build problems trying to build for an IBM Power9 system

[austinpagan]

Running into build problems trying to build for an IBM Power9 system

[austinpagan]

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

[austinpagan]

I am but an egg, but I'm guessing the plugins need the same treatment you gave the main library?

[Eigenstate]

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!

[austinpagan]

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
'test': VMDTest,
File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "setup.py", line 39, in run
self.execute(self.compile_vmd, [], msg="Compiling VMD")
File "/usr/lib64/python2.7/distutils/cmd.py", line 349, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/usr/lib64/python2.7/distutils/util.py", line 324, in execute
func(*args)
File "setup.py", line 59, in compile_vmd
check_call(cmd, cwd=srcdir)
File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/vmd-1.9.3/vmd-python/vmd/install.sh', 'LINUX', '/vmd-1.9.3/vmd-python/build/lib/vmd', '/usr']' returned non-zero exit status 2
[root@234bc51125a5 vmd-python]#

[Eigenstate]

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()"?

[austinpagan]

You had some typos, but here's what I think you want:

$ python -c "import platform; print(platform.system(), platform.machine())"
('Linux', 'ppc64le')
$

[austinpagan]

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.

[austinpagan]

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?

[Eigenstate]

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.

[austinpagan]

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.

[austinpagan]

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?

[austinpagan]

For future reference, can you point me to the EGL/egl.h and the libOpenGL.so?

[Eigenstate]

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

[austinpagan]

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"

[austinpagan]

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
'test': VMDTest,
File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "setup.py", line 66, in run
self.execute(self.compile_vmd, [], msg="Compiling VMD")
File "/usr/lib64/python2.7/distutils/cmd.py", line 349, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/usr/lib64/python2.7/distutils/util.py", line 324, in execute
func(*args)
File "setup.py", line 77, in compile_vmd
self.set_environment_variables(pydir)
File "setup.py", line 284, in set_environment_variables
os.environ["SQLITELIB"] = "-L%s" % self._find_library_dir("libsqlite3")
File "setup.py", line 201, in _find_library_dir
libfile);
RuntimeError: Could not find library 'libsqlite3.so' in standard library directories. Update $LD_LIBRARY_PATH to include the directory containing this file, or make sure it is present on your system
[fossum@fstgbfen1 vmd-python]$

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]$

[austinpagan]

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

?

[austinpagan]

"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?

[jvermaas]

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.

[austinpagan]

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

[jvermaas]

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?

[austinpagan]

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?

[austinpagan]

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?

[jvermaas]

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

[austinpagan]

[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]#

[jvermaas]

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.

[austinpagan]

Yes, thank you! I now am trying to build and install your version. More info soon.

[Eigenstate]

I merged @jvermaas pull request so you can also try the ppc64le branch again

[austinpagan]

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

[jvermaas]

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.

[austinpagan]

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

[austinpagan]

Maybe you can suggest a "hello world" program I can try to see if vmd is actually working?

[austinpagan]

And maybe there's no defined "help screen" for vmd yet?

[austinpagan]

ERASE ERASE ERASE
I was not aware that you have to import a package before you can call help on the package.
"help(vmd)" actually returns useful stuff!

[jvermaas]

from vmd import evaltcl
evaltcl('vmdinfo version')

Would be the basic test. Glad you got the import sorted. :)

[austinpagan]

from vmd import evaltcl
evaltcl('vmdinfo version')
'1.9.4a26'

[austinpagan]

So, moving on to the next phase:
@Eigenstate ... my manager is going to see your comments that EGL is supported and he's going to wonder why I can't just do the build specifying the "--egl" flag, as you indicated in your README. But I'm thinking that flag is only valid on Debian systems? When I tried it I got an error.

[Eigenstate]

What's the error message? You'll need to install the header file and library dependencies for EGL in order for the build to succeed:

• GL/gl.h
• EGL/egl.h, EGL/eglext.h
• libOpenGL.so

On Centos, you can use yum whatprovides or similar to find which package names provide these dependencies. The naming can differ between distros so I only list the packages for Debian which is what I run personally.

[austinpagan]

My manager went to a lot of effort to ensure that EGL was enabled on this box:

[root@f52816e1f650 vmd-python]# ls /usr/local/include/GL/gl.h
/usr/local/include/GL/gl.h
[root@f52816e1f650 vmd-python]# ls /usr/local/include/EGL/*
/usr/local/include/EGL/eglext.h /usr/local/include/EGL/egl.h /usr/local/include/EGL/eglplatform.h
[root@f52816e1f650 vmd-python]# ls /lib64/libOpenGL*
/lib64/libOpenGL.so /lib64/libOpenGL.so.0 /lib64/libOpenGL.so.0.0.0
[root@f52816e1f650 vmd-python]#

Here's the error I get:

[root@f52816e1f650 vmd-1.9.3]# rm -rf vmd-python
[root@f52816e1f650 vmd-1.9.3]# git clone --branch ppc64le https://github.com/Eigenstate/vmd-python
Cloning into 'vmd-python'...
remote: Enumerating objects: 86, done.
remote: Counting objects: 100% (86/86), done.
remote: Compressing objects: 100% (59/59), done.
remote: Total 9078 (delta 52), reused 53 (delta 27), pack-reused 8992
Receiving objects: 100% (9078/9078), 39.15 MiB | 19.04 MiB/s, done.
Resolving deltas: 100% (3760/3760), done.
[root@f52816e1f650 vmd-1.9.3]# cd vmd-python
[root@f52816e1f650 vmd-python]# python setup.py --egl build
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: option --egl not recognized
[root@f52816e1f650 vmd-python]#

[jvermaas]

Try it the other way around. python setup.py build --egl

[austinpagan]

It's compiling. I suppose if the requisite OpenGL and EGL include/libs are in bad directories, I can get past that with some environment variables?

[austinpagan]

echo "Linking " libvmd.so "...";
cd ../LINUXPPC64 ;
g++ -m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -fPIC -DVMD_SHARED -DARCH_LINUXPPC64 -DVMDOPENGLPBUFFER -DVMDEGLPBUFFER -DVMDCOLVARS -DVMDIMD -DVMDPYTHON -DVMDTHREADS -DWKFTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -DVMDNUMPY -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDLATTICECUBES -DVMDTCL -DVMDSTATICPLUGINS -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/lib64/python2.7/site-packages/numpy/core/lib -I/usr/include/ -I../plugins/include -I../plugins/LINUXPPC64/molfile -I/usr/include/ -I. -I../src -o libvmd.so OpenGLPbufferDisplayDevice.o OpenGLExtensions.o OpenGLRenderer.o OpenGLShader.o OpenGLCache.o colvaratoms.o colvarbias.o colvarbias_abf.o colvarbias_alb.o colvarbias_histogram.o colvarbias_meta.o colvarbias_restraint.o colvar.o colvarcomp.o colvarcomp_angles.o colvarcomp_coordnums.o colvarcomp_distances.o colvarcomp_protein.o colvarcomp_rotations.o colvardeps.o colvargrid.o colvarmodule.o colvarparse.o colvarproxy.o colvarproxy_vmd.o colvarscript.o colvartypes.o colvarvalue.o IMDMgr.o IMDSim.o IMDSimThread.o CmdIMD.o imd.o PythonTextInterp.o VMDTkinterMenu.o py_animate.o py_atomsel.o py_axes.o py_color.o py_commands.o py_display.o py_graphics.o py_imd.o py_label.o py_material.o py_measure.o py_menu.o py_molecule.o py_molrep.o py_mouse.o py_render.o py_selection.o py_topo.o py_trans.o py_vmd.o py_numeric.o androidvmdstart.o Animation.o ArtDisplayDevice.o AtomColor.o AtomParser.o AtomLexer.o AtomRep.o AtomSel.o Axes.o BaseMolecule.o Benchmark.o BondSearch.o CmdAnimate.o CmdColor.o CmdDisplay.o CmdLabel.o CmdMaterial.o CmdMenu.o CmdMol.o CmdRender.o CmdTrans.o CommandQueue.o CoorPluginData.o CUDAAccel.o DisplayDevice.o Displayable.o DisplayRocker.o DispCmds.o DrawMolecule.o DrawMolItem.o DrawMolItem2.o DrawMolItemRibbons.o DrawMolItemMSMS.o DrawMolItemNanoShaper.o DrawMolItemRings.o DrawMolItemOrbital.o DrawMolItemQuickSurf.o DrawMolItemSurface.o DrawMolItemVolume.o DrawForce.o DrawRingsUtils.o FastPBC.o FileRenderList.o FileRenderer.o FPS.o GaussianBlur.o GelatoDisplayDevice.o GeometryAngle.o GeometryAtom.o GeometryBond.o GeometryDihedral.o GeometryList.o GeometryMol.o GeometrySpring.o Hershey.o HMDMgr.o Inform.o ImageIO.o Isosurface.o JRegex.o JString.o macosxvmdstart.o MaterialList.o Matrix4.o MayaDisplayDevice.o MDFF.o Measure.o MeasureCluster.o MeasurePBC.o MeasureRDF.o MeasureQCP.o MeasureSurface.o MeasureSymmetry.o MeasureVolInterior.o MobileInterface.o MobileButtons.o MobileTracker.o Molecule.o MoleculeList.o MoleculeGraphics.o MolFilePlugin.o Mouse.o MSMSInterface.o NanoShaperInterface.o Orbital.o OrbitalJIT.o PeriodicTable.o P_JoystickTool.o P_TugTool.o P_GrabTool.o P_PrintTool.o P_PinchTool.o P_UIVR.o P_Buttons.o P_Tracker.o P_Tool.o P_CmdTool.o P_SensorConfig.o ParseTree.o PickList.o PickModeAddBond.o PickModeCenter.o PickModeForce.o PickModeList.o PickModeMolLabel.o PickModeMove.o PickModeUser.o PlainTextInterp.o PluginMgr.o POV3DisplayDevice.o PSDisplayDevice.o QMData.o QMTimestep.o QuickSurf.o RadianceDisplayDevice.o RayShadeDisplayDevice.o R3dDisplayDevice.o RenderManDisplayDevice.o Scene.o ScaleSpaceFilter.o Segmentation.o SnapshotDisplayDevice.o Spaceball.o SpaceballButtons.o SpaceballTracker.o SpatialSearch.o SpringTool.o Stage.o STLDisplayDevice.o Stride.o Surf.o SymbolTable.o TachyonDisplayDevice.o Timestep.o UIObject.o UIText.o VideoStream.o VMDApp.o VMDCollab.o VMDDir.o VMDDisplayList.o VMDMenu.o VMDQuat.o VMDTitle.o VMDThreads.o VolCPotential.o VolMapCreate.o VolMapCreateILS.o VolumetricData.o VolumeTexture.o Voltool.o VrmlDisplayDevice.o Vrml2DisplayDevice.o Watershed.o WavefrontDisplayDevice.o WKFThreads.o WKFUtils.o utilities.o util_simd.o vmd.o vmdmain.o X3DDisplayDevice.o ColorInfo.o TclCommands.o TclFastPBC.o TclMDFF.o TclMeasure.o TclMolInfo.o TclTextInterp.o TclVec.o TclGraphics.o TclSegmentation.o TclVolMap.o TclVoltool.o cmd_animate.o cmd_collab.o cmd_color.o cmd_display.o cmd_imd.o cmd_label.o cmd_material.o cmd_menu.o cmd_mobile.o cmd_mol.o cmd_mouse.o cmd_parallel.o cmd_plugin.o cmd_profile.o cmd_render.o cmd_spaceball.o cmd_tool.o cmd_trans.o cmd_user.o cmd_util.o cmd_videostream.o cmd_vmdbench.o tcl_commands.o VMDTkMenu.o hash.o inthash.o intstack.o ptrstack.o msmpot.o msmpot_compute.o msmpot_cubic.o msmpot_setup.o vmdsock.o vmddlopen.o pcre.o fitrms.o -L/usr/lib/python2.7/site-packages -L/usr/lib64/ -L../plugins/LINUXPPC64/molfile -L/usr/lib64/ -lEGL -L/usr/X11R6/lib -lGL -lXext -lX11 -lpthread -ltcl8.5 -lmolfile_plugin -lnetcdf -lm -ldl -lsqlite3 -lexpat -L/usr/lib64 -lpython2.7 -Wl,-rpath,/usr/X11R6/lib -Wl,-rpath,/usr/local/lib -shared ;
Linking libvmd.so ...
/usr/bin/ld: cannot find -lGL
/usr/bin/ld: cannot find -lXext
collect2: error: ld returned 1 exit status

[Eigenstate]

Looks like the build is pulling in the wrong libraries. Let me take a look.

[austinpagan]

Here in flyover country it's nearly 9PM, so I'll check back here at 7AM tomorrow (5AM your time).
Thanks SO MUCH for enabling this functionality for us!

[austinpagan]

Just to be clear, we believe (based on your README) that EGL is a prerequisite for using offscreen "pbuffers," and we believe that pbuffers are pretty much mandatory for visualization in any environment that doesn't have a local windowing system (like large clusters of servers). Is that correct? Because if not, we are open to other options...

[jvermaas]

Just curious, but what happens when you do the following:

from vmd import render
print render.listall()

VMD has plenty of rendering capabilities that depend on external programs. In principle you could use the render pipeline and those external programs to make images if you choose, and I don't think that those require OpenGL at all, although I may be quite mistaken.

[austinpagan]

from vmd import render
print render.listall()
['ART', 'Gelato', 'PostScript', 'Raster3D', 'Radiance', 'Rayshade', 'RenderMan', 'snapshot', 'STL', 'Tachyon', 'POV3', 'VRML-1', 'VRML-2', 'Wavefront', 'X3D', 'X3DOM']

[austinpagan]

I had been using "snapshot" to capture things stored in pbuffers and output them to a .tga file.
One program I had recently done (using vmd directly) looked like this:

vmd -dispdev openglpbuffer
vmd> mol new proteins/alanin.pdb
vmd> graphics 0 cylinder {1 1 1} {2 2 2} radius 2 resolution 60 filled no
vmd> graphics 0 color 3
vmd> graphics 0 cylinder {3 3 3} {4 4 4} radius 2 resolution 60 filled no
vmd> render snapshot firstfile.tga

[jvermaas]

Weird. Even with -dispdev text normal VMD can render just fine, but I tried it myself and vmd-python can't quite do that the way I compiled it (without egl stuff). So it looks like that option has a purpose after all.

[austinpagan]

I inquired of my manager, regarding the reasoning behind our focus on EGL. He told me this, which I share with you to help explain our understanding of the importance of EGL:

Here is the general strategy: If running on client system, then use whatever window system is appropriate for your client, otherwise (on a server) use EGL. EGL is not a replacement for OpenGL. It is just a way to initialize the GPU, select a visual, etc without the heavyweight and non-secure X-server.

[austinpagan]

I'm not in a hurry here, and I'm sure you have many things that are higher priority, but could I get a warm fuzzy that you're still hoping to provide an update for me to try?

[Eigenstate]

At some point, yes, but timing is likely to be on the order of weeks. All that needs to be done is getting setuptools/distutils to get the right flags to the actual build, but setuptools is a mess and getting build/install to both work has been pretty time consuming and I need to do my actual work.

You're welcome to mess with setup.py to get it working and I'd be happy to merge any pull requests you send my way.

[austinpagan]

I am serene about this. I've never seen a "setup.py" file before, but I shall take this as my opportunity to bootstrap myself into a working level of knowledge about all things "python module distribution." I'm not confident that I'll be successful, but it's better than waiting.

I will say, I'm also unschooled in the concept of a "pull request," so I may just ship you my version of setup.py in an email, if I get it running... hope that's OK?

[austinpagan]

I've deleted my previous comment.
I'm still seeing the problem.
I had accidentally built it without the "--egl" flag. When I include that flag, I'm back to where I was before... sorry for the confusion.

[Eigenstate]

Alright I've fixed the build so the flags propagate correctly.
I've merged the ppc64le changes, so now we're on a new branch called egl and you won't have to build and install separately.

git checkout egl
python setup.py --egl install

If it doesn't work, rebuild to get debug output and paste what you get when you import vmd:
python setup.py --egl --debug install

[austinpagan]

Sorry, but I'm not very experienced with github... here's what I did:

[root@f48872560257 vmd-python]# pwd
/vmd-1.9.3/vmd-python
[root@f48872560257 vmd-python]# ls -a
. .binstar.yml .bumpversion.cfg .git LICENSE meta.yaml setup.py .travis.yml
.. build docs .gitignore MANIFEST.in README.md test vmd
[root@f48872560257 vmd-python]# git checkout egl
error: pathspec 'egl' did not match any file(s) known to git.
[root@f48872560257 vmd-python]#

[austinpagan]

instead, I tried this:

git clone --branch egl https://github.com/Eigenstate/vmd-python
cd vmd-python
python setup.py --egl install

This is building... will advise.

[austinpagan]

So, it eventually died, complaining that it couldn't find GL and Xext.
I did the debug version, and here's that output:

[root@f48872560257 vmd-python]# python setup.py --egl --debug install
running install
running build
Finding libraries...
LIB: libtcl8.5.so -> /usr/lib64/
INC: tcl.h -> /usr/include/
LIB: libsqlite3.so -> /usr/lib64/
INC: sqlite3.h -> /usr/include/
LIB: libexpat.so -> /usr/lib64/
INC: expat.h -> /usr/include/
LIB: libnetcdf.so -> /usr/lib64/
INC: netcdf.h -> /usr/include/
Building with debug symbols
Traceback (most recent call last):
File "setup.py", line 451, in
'test': VMDTest,
File "/usr/lib/python2.7/site-packages/setuptools/init.py", line 143, in setup
return distutils.core.setup(**attrs)
File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "setup.py", line 417, in run
self.run_command("build")
File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "setup.py", line 71, in run
self.compile_vmd()
File "setup.py", line 85, in compile_vmd
self.set_environment_variables(pydir)
File "setup.py", line 332, in set_environment_variables
asandir = self._find_library_dir("libasan")
File "setup.py", line 216, in _find_library_dir
libfile);
RuntimeError: Could not find library 'libasan.so' in standard library directories. Update $LD_LIBRARY_PATH to include the directory containing this file, or make sure it is present on your system
[root@f48872560257 vmd-python]#

[austinpagan]

Notably, when I cleared out the directory, re-cloned it, and tried to build with the debug, it died instantly the same way, rather than building a bunch of stuff for ten minutes. I wonder if there's a bug in the usage of the '--debug' flag...

[damora]

@austinpagan have you verified that you have this library somewhere on the system?
RuntimeError: Could not find library 'libasan.so' in standard library directories. Update $LD_LIBRARY_PATH to include the directory containing this file, or make sure it is present on your system

[austinpagan]

"ls -ltR | grep libasan" from the root directory returns nothing.

"yum install libasan" says there's no such package.

Jeff found an rpm: libasan-9.0.1-0.8.fc30.ppc64le.rpm

We tried "rpm -i libasan-9.0.1-0.8.fc30.ppc64le.rpm" and it said:

warning: libasan-9.0.1-0.8.fc30.ppc64le.rpm: Header V3 RSA/SHA256 Signature, key ID 3c3359c4: NOKEY
error: Failed dependencies:
libm.so.6(GLIBC_2.23)(64bit) is needed by libasan-9.0.1-0.8.fc30.ppc64le

I then tried "yum localinstall libasan-9.0.1-0.8.fc30.ppc64le.rpm", and it got further, but eventually also said:

Error: Package: libasan-9.0.1-0.8.fc30.ppc64le (/libasan-9.0.1-0.8.fc30.ppc64le)
Requires: libm.so.6(GLIBC_2.23)(64bit)

I tried to search for anything that contained the string "libm.":

[root@f48872560257 vmd-1.9.3]# yum search 'libm.'
Loaded plugins: fastestmirror, ovl
Loading mirror speeds from cached hostfile

• base: mirror.siena.edu
• epel: fedora-epel.mirrors.tds.net
• extras: mirror.siena.edu
• updates: mirror.siena.edu
  Warning: No matches found for: libm.
  No matches found
  [root@f48872560257 vmd-1.9.3]#

So I'm stumped...

[austinpagan]

I looked into building libasan (which apparently is a package called "Address Sanitizer") from source.
The web page https://github.com/google/sanitizers/wiki/AddressSanitizerHowToBuild told me to do:
svn co http://llvm.org/svn/llvm-project/llvm/trunk llvm
But "svn" is not found on my system.
I did a "yum search" on "svn" and found a package called "git-svm".
I did a "yum install" on "git-svm".
Now, svn is on my system, and "svn co http://llvm.org/svn/llvm-project/llvm/trunk llvm" checked out a bunch of code!
The next step involved "cmake" but it failed saying I needed cmake version 3.4.3, but yum tells me that my version (2.8.12) is the latest available.

So, I'm stumped AGAIN.

[Eigenstate]

Don't worry about building ASAN - it's a library used to help me debug things but won't help with your specific problem. I know what's going on, just hold off on doing anything until I can fix it. If you could paste the output of what "complaining it can't find GL and Xext" that would be helpful.

[austinpagan]

I am so sorry that I did not notice you posted this reply. I trust my work email to notify me of these things, and it let me down... sigh

The last lines before the error look like this:

Compiling hash.c --> hash.o ...
Compiling inthash.c --> inthash.o ...
Compiling intstack.c --> intstack.o ...
Compiling ptrstack.c --> ptrstack.o ...
Compiling msmpot.c --> msmpot.o ...
Compiling msmpot_compute.c --> msmpot_compute.o ...
Compiling msmpot_cubic.c --> msmpot_cubic.o ...
Compiling msmpot_setup.c --> msmpot_setup.o ...
Compiling vmdsock.c --> vmdsock.o ...
vmdsock.c: In function ‘vmdsock_accept’:
vmdsock.c:133:30: warning: pointer targets in passing argument 3 of ‘accept’ differ in signedness [-Wpointer-sign]
rc = accept(s->sd, (struct sockaddr *) &s->addr, &len);
^
In file included from /usr/include/netinet/in.h:24:0,
from /usr/include/arpa/inet.h:22,
from vmdsock.c:35:
/usr/include/sys/socket.h:244:12: note: expected ‘socklen_t * restrict’ but argument is of type ‘int *’
extern int accept (int __fd, __SOCKADDR_ARG __addr,
^
Compiling vmddlopen.c --> vmddlopen.o ...
Compiling pcre.c --> pcre.o ...
Compiling fitrms.c --> fitrms.o ...
Linking libvmd.so ...
/usr/bin/ld: cannot find -lGL
/usr/bin/ld: cannot find -lXext
collect2: error: ld returned 1 exit status

[austinpagan]

On this system, I find these libraries here:

[root@f48872560257 lib64]# pwd
/usr/lib64
[root@f48872560257 lib64]# ls libGL.*
libGL.so.1 libGL.so.1.7.0
[root@f48872560257 lib64]# ls libXext.*
libXext.so.6 libXext.so.6.4.0
[root@f48872560257 lib64]#

[damora]

/usr/lib64/nvidia/

[austinpagan]

@damora I was hoping for a verb... (shy smile)
So, in /usr/lib64, I did "mkdir nvidia".
Then I copied the two libraries into that new directory.
Then I re-created the links to those libraries to mirror what was happening in the original directory.
Then I cleared out the vmd-python directory, and cloned a fresh one.
When I rebuilt, it gave me the exact same error as I documented above.
I shall now wait for wisdom from the package author, unless I misinterpreted your message, and you can clarify for me...

[austinpagan]

I woke with an inspiration. Maybe I also needed to create links that ended in .so (or perhaps .a)?
So I created those links (both in /usr/lib64 and /usr/lib64/nvidia), and now the command
python setup.py --egl install
ends like this:

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
running egg_info
creating vmd_python.egg-info
writing vmd_python.egg-info/PKG-INFO
writing top-level names to vmd_python.egg-info/top_level.txt
writing dependency_links to vmd_python.egg-info/dependency_links.txt
writing manifest file 'vmd_python.egg-info/SOURCES.txt'
reading manifest file 'vmd_python.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'bld.bat'
warning: no files found matching 'build.sh'
no previously-included directories found matching 'vmd/vmd_src/LINUXAMD64'
no previously-included directories found matching 'vmd/plugins/build'
writing manifest file 'vmd_python.egg-info/SOURCES.txt'
Copying vmd_python.egg-info to /usr/lib/python2.7/site-packages/vmd_python-3.0.2-py2.7.egg-info
running install_scripts
[root@f48872560257 vmd-python]#

Does that look like a proper end to the process?

I will now go rooting around for test programs to run, to see if this is all properly built.

[austinpagan]

I started a "python session" and typed in the first couple of lines from your README:
from vmd import molecule, vmdnumpy
import numpy as np
mask = vmdnumpy.atomselect(molid_avg, 0, "resname TYR")

The first command resulted in this:

[root@f48872560257 vmd-python]# 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.

from vmd import molecule, vmdnumpy
/usr/lib/python2.7/site-packages/vmd/init.py:17: UserWarning: Module vmd was already imported from /usr/lib/python2.7/site-packages/vmd/init.pyc, but /vmd-1.9.3/vmd-python is being added to sys.path
from pkg_resources import resource_filename
Info) EGL: node[0] bound to display[0], 4 displays total

Then followed a pile of warnings that looked like this:

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

Then, the next two commands looked like this:

import numpy as np
mask = vmdnumpy.atomselect(molid_avg, 0, "resname TYR")
Traceback (most recent call last):
File "", line 1, in
NameError: name 'molid_avg' is not defined

Are those warnings OK?
Does your distribution have any sample molecules I can use?

[austinpagan]

Also, I removed the "nvidia" directory from /usr/lib64, as the comment from @damora was intended for a different experiment I was trying, not documented in this stream, and I misunderstood him. My apologies.

[austinpagan]

Here's the list of links that got me past the problem:

[root@f48872560257 lib64]# ls -lt libGL.*
lrwxrwxrwx 1 root root 14 Mar 18 11:32 libGL.a -> libGL.so.1.7.0
lrwxrwxrwx 1 root root 14 Mar 18 11:31 libGL.so -> libGL.so.1.7.0
lrwxrwxrwx 1 root root 14 Jan 23 16:15 libGL.so.1 -> libGL.so.1.7.0
-rwxr-xr-x 1 root root 803280 Oct 30 21:26 libGL.so.1.7.0
[root@f48872560257 lib64]# ls -lt libXext.*
lrwxrwxrwx 1 root root 16 Mar 18 11:32 libXext.a -> libXext.so.6.4.0
lrwxrwxrwx 1 root root 16 Mar 18 11:31 libXext.so -> libXext.so.6.4.0
lrwxrwxrwx 1 root root 16 Jan 23 16:15 libXext.so.6 -> libXext.so.6.4.0
-rwxr-xr-x 1 root root 137232 Nov 22 2015 libXext.so.6.4.0
[root@f48872560257 lib64]#

[austinpagan]

On the same day that I created this problem, you commented as follows:

"Remove PBuffer support for now as getting a universal build is tricky
I need libOpenGL.so to link against for headless systems, but it's
not readily available on a lot of distros (including Travis' Ubuntu 14).
Also, there's no conda package for it, so I'm tabling this for now"

Is this also true in our "egl" branch? If not, could you show me a version
of the "render" test that I could use to try rendering something to a PBuffer?