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Running into build problems trying to build for an IBM Power9 system #22

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Running into build problems trying to build for an IBM Power9 system#22

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@austinpagan
austinpagan
opened on Feb 22, 2019

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.

Activity

  1. Eigenstate commented on Feb 22, 2019

    @Eigenstate
    Eigenstate
    on Feb 22, 2019
    Owner

    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!

  2. austinpagan commented on Feb 22, 2019

    @austinpagan
    austinpagan
    on Feb 22, 2019
    Author

    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]#

  3. austinpagan
    changed the title [-]Running into build problems trying to build for an IBM Power8 system[/-] [+]Running into build problems trying to build for an IBM Power9 system[/+] on Feb 22, 2019

  4. Eigenstate commented on Feb 22, 2019

    @Eigenstate
    Eigenstate
    on Feb 22, 2019
    Owner

    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()"?

  5. austinpagan commented on Feb 22, 2019

    @austinpagan
    austinpagan
    on Feb 22, 2019
    Author

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

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

  6. austinpagan commented on Feb 23, 2019

    @austinpagan
    austinpagan
    on Feb 23, 2019
    Author

    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.

  7. austinpagan commented on Feb 23, 2019

    @austinpagan
    austinpagan
    on Feb 23, 2019
    Author

    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?

  8. Eigenstate commented on Feb 25, 2019

    @Eigenstate
    Eigenstate
    on Feb 25, 2019
    Owner

    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.

  9. austinpagan commented on Feb 26, 2019

    @austinpagan
    austinpagan
    on Feb 26, 2019
    Author

    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.

  10. austinpagan commented on Feb 26, 2019

    @austinpagan
    austinpagan
    on Feb 26, 2019
    Author

    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?

  11. austinpagan commented on Feb 26, 2019

    @austinpagan
    austinpagan
    on Feb 26, 2019
    Author

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

  12. Eigenstate commented on Feb 26, 2019

    @Eigenstate
    Eigenstate
    on Feb 26, 2019
    Owner

    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

  13. austinpagan commented on Feb 26, 2019

    @austinpagan
    austinpagan
    on Feb 26, 2019
    Author

    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"

  14. austinpagan commented on Feb 27, 2019

    @austinpagan
    austinpagan
    on Feb 27, 2019
    Author

    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]$

  15. austinpagan commented on Feb 27, 2019

    @austinpagan
    austinpagan
    on Feb 27, 2019
    Author

    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

    ?

  16. 42 remaining items

  17. austinpagan commented on Mar 13, 2019

    @austinpagan
    austinpagan
    on Mar 13, 2019
    Author

    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]#

  18. austinpagan commented on Mar 13, 2019

    @austinpagan
    austinpagan
    on Mar 13, 2019
    Author

    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...

  19. damora commented on Mar 14, 2019

    @damora
    damora
    on Mar 14, 2019

    @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

  20. austinpagan commented on Mar 14, 2019

    @austinpagan
    austinpagan
    on Mar 14, 2019
    Author

    "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...

  21. austinpagan commented on Mar 14, 2019

    @austinpagan
    austinpagan
    on Mar 14, 2019
    Author

    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.

  22. Eigenstate commented on Mar 14, 2019

    @Eigenstate
    Eigenstate
    on Mar 14, 2019
    Owner

    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.

  23. austinpagan commented on Mar 17, 2019

    @austinpagan
    austinpagan
    on Mar 17, 2019
    Author

    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

  24. austinpagan commented on Mar 17, 2019

    @austinpagan
    austinpagan
    on Mar 17, 2019
    Author

    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]#

  25. damora commented on Mar 18, 2019

    @damora
    damora
    on Mar 18, 2019

    /usr/lib64/nvidia/

  26. austinpagan commented on Mar 18, 2019

    @austinpagan
    austinpagan
    on Mar 18, 2019
    Author

    @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...

  27. austinpagan commented on Mar 18, 2019

    @austinpagan
    austinpagan
    on Mar 18, 2019
    Author

    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.

  28. austinpagan commented on Mar 18, 2019

    @austinpagan
    austinpagan
    on Mar 18, 2019
    Author

    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?

  29. austinpagan commented on Mar 18, 2019

    @austinpagan
    austinpagan
    on Mar 18, 2019
    Author

    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.

  30. austinpagan commented on Mar 18, 2019

    @austinpagan
    austinpagan
    on Mar 18, 2019
    Author

    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]#

  31. austinpagan commented on Mar 20, 2019

    @austinpagan
    austinpagan
    on Mar 20, 2019
    Author

    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?

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