openchemistry / molequeue

Desktop integration of high performance computing resources

MoleQueue

Introduction

MoleQueue is an open-source, cross-platform, system-tray resident desktop application for abstracting, managing, and coordinating the execution of tasks both locally and on remote computational resources. Users can set up local and remote queues that describe where the task will be executed. Each queue can have programs, with templates to facilitate the execution of the program. Input files can be staged, and output files collected using a standard interface. Some highlights:

• Open source distributed under the liberal 3-clause BSD license
• Cross platform with nightly builds on Linux, Mac OS X and Windows
• Intuitive interface designed to be useful to whole community
• Support for local executation and remote schedulers (SGE, PBS, SLURM)
• System tray resident application managing queue of queues and job lifetime
• Simple, lightweight JSON-RPC 2.0 based communication over local sockets
• Qt 5 client library for simple integration in Qt applications

MoleQueue is being developed as part of the Open Chemistry project at Kitware, along with companion tools and libraries to support the work.

Installing

We provide nightly binaries built by our dashboards for Mac OS X and Windows. If you would like to build from source we recommend that you follow our building Open Chemistry guide that will take care of building most dependencies.

Contributing

Our project uses the standard GitHub pull request process for code review and integration. Please check our development guide for more details on developing and contributing to the project. The GitHub issue tracker can be used to report bugs, make feature requests, etc.

Our wiki is used to document features, flesh out designs and host other documentation. Our API is documented using Doxygen with updated documentation generated nightly. We have several mailing lists to coordinate development and to provide support.

molequeue's Issues

molequeue/app/program.cpp: 2 * missing field init in copy-ctor ?

molequeue/app/program.cpp:46:10: warning: Member variable 'Program::m_queueManager' is not initialized in the copy constructor. [uninitMemberVar]

molequeue/app/program.cpp:46:10: warning: Member variable 'Program::m_server' is not initialized in the copy constructor. [uninitMemberVar]

Translations

Would you please advise how translations are provided to the MoleQueue project?

Are they done with Weblate, like Avogadro?

Thank you

OpenChemistry/avogadroapp#218 (comment)

Cut new release 0.8.0 tarball

We wish to use molequeue in Gentoo. The current 0.7.1 release is marred with issues due to the bundled Qt5 JSON library clashing with installed Qt5 headers. In addition, for 0.7.1, the library is not compatible Qt5, only Qt4. For 0.8.0 you have ported the library to Qt5. Could you please cut a tarball of the source for us and place it on Sourceforge, seeing you have 0.8.0 Windows Installer at Sourceforge. Thanks a lot!

Fails to submit the GAMESS job: Please select the target program from the "Queue and Program" list.

The "Queue and Program" list is empty.

Installing fails when using DESTDIR

Hi, I'm trying to add molequeue 0.9.0 to MacPorts, as requested years ago. It builds, but installing fails because MacPorts does something like make install DESTDIR=/path/to/destroot which results in:

-- fixup_qt5_executable
--   executable='/path/to/destroot/opt/local/MoleQueue.app'
--   qtplugins=''
--   libs='/path/to/destroot/opt/local/MoleQueue.app/Contents/PlugIns/platforms/libqcocoa.dylib'
--   dirs='/opt/local/lib;/opt/local/share/cmake/Modules/bin;/opt/local/share/cmake/Modules/lib;/opt/local/libexec/qt5/lib/QtCore.framework'
--   plugins_dir='lib/molequeue/plugins'
--   request_qt_conf=''
-- Writing /path/to/destroot/opt/local/MoleQueue.app/Contents/Resources/qt.conf
-- fixup_bundle
--   app='/path/to/destroot/opt/local/MoleQueue.app'
--   libs='/path/to/destroot/opt/local/MoleQueue.app/Contents/PlugIns/platforms/libqcocoa.dylib'
--   dirs='/opt/local/lib;/opt/local/share/cmake/Modules/bin;/opt/local/share/cmake/Modules/lib;/opt/local/libexec/qt5/lib/QtCore.framework'
--   ignoreItems=''
-- fixup_bundle: preparing...
--
warning: cannot resolve item '/opt/local/lib/libMoleQueueServerCore.dylib'

  possible problems:
    need more directories?
    need to use InstallRequiredSystemLibraries?
    run in install tree instead of build tree?

--
warning: cannot resolve item '/opt/local/lib/libMoleQueueClient.dylib'

  possible problems:
    need more directories?
    need to use InstallRequiredSystemLibraries?
    run in install tree instead of build tree?

--
warning: cannot resolve item '/opt/local/lib/libMoleQueueClient.dylib'

  possible problems:
    need more directories?
    need to use InstallRequiredSystemLibraries?
    run in install tree instead of build tree?

CMake Error at /opt/local/share/cmake-3.15/Modules/BundleUtilities.cmake:452 (message):
  otool -l failed: 1

  /Library/Developer/CommandLineTools/usr/bin/objdump:
  '/opt/local/lib/libMoleQueueClient.dylib': No such file or directory

Call Stack (most recent call first):
  /opt/local/share/cmake-3.15/Modules/BundleUtilities.cmake:521 (get_item_rpaths)
  /opt/local/share/cmake-3.15/Modules/BundleUtilities.cmake:659 (set_bundle_key_values)
  /opt/local/share/cmake-3.15/Modules/BundleUtilities.cmake:939 (get_bundle_keys)
  /path/to/molequeue-0.9.0/cmake/DeployQt5.cmake:199 (fixup_bundle)
  molequeue/lastinstall/cmake_install.cmake:42 (fixup_qt5_executable)
  molequeue/cmake_install.cmake:41 (include)
  cmake_install.cmake:71 (include)


make: *** [install/fast] Error 1

fixup_qt5_executable is apparently expecting the libraries to have been installed in their final destination already, but they have not been; they are in the destroot.

Libraries with soname

Hi all.

Currently, moleque libraries are unversioned. Please, consider to create versioned libraries in order to prevent incompatibilities.

cmake/GenerateExportHeader.cmake update for GCC 6

This should be relevant for every library with this file (avogadrolibs, others?).

diff --git a/cmake/GenerateExportHeader.cmake b/cmake/GenerateExportHeader.cmake
index a91da06..3dd14ed 100644
--- a/cmake/GenerateExportHeader.cmake
+++ b/cmake/GenerateExportHeader.cmake
@@ -164,12 +164,12 @@ macro(_test_compiler_hidden_visibility)
   if(CMAKE_COMPILER_IS_GNUCXX)
     exec_program(${CMAKE_C_COMPILER} ARGS --version
       OUTPUT_VARIABLE _gcc_version_info)
-    string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]"
+    string(REGEX MATCH "[3456]\\.[0-9]\\.[0-9]"
       _gcc_version "${_gcc_version_info}")
     # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
     # patch level, handle this here:
     if(NOT _gcc_version)
-      string(REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0"
+      string(REGEX REPLACE ".*\\(GCC\\).* ([3456]\\.[0-9]) .*" "\\1.0"
         _gcc_version "${_gcc_version_info}")
     endif()

Port to Qt6

I couldn't build avogadro+qt6+molequeue because molequeue still depends on Qt5

Failed version check for GCC 7

This is the same problem as #7, but for GCC 7.

The sever listens on MoleQueue but the python client connects on zmq_MoleQueue

Names should match, obviously.

At least three files have Python syntax errors

$ flake8 . --count --select=E9,F63,F7 --show-source --statistics

./molequeue/python/test/clienttest.py:24:11: E999 SyntaxError: invalid syntax
    print "MoleQueue ID: ", molequeue_id
          ^
./molequeue/molequeue/app/testing/scripts/submitJob.py:19:11: E999 SyntaxError: invalid syntax
    print "Client %s connecting to socket: %s"%(clientId, socketname)
          ^
./molequeue/molequeue/app/testing/scripts/sendRpcKill.py:13:11: E999 SyntaxError: invalid syntax
    print "Connecting to socket: %s"%socketname
          ^
3     E999 SyntaxError: invalid syntax
3