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Desktop integration of high performance computing resources

Home Page: http://openchemistry.org/molequeue

License: BSD 3-Clause "New" or "Revised" License

CMake 4.12% C++ 92.72% Python 1.58% Shell 1.57%

molequeue's Introduction

Open Chemistry

Introduction

The Open Chemistry project is a collection of open source, cross platform libraries and applications for the exploration, analysis and generation of chemical data. The project builds upon various efforts by collaborators and innovators in open chemistry such as the Blue Obelisk, Quixote and the associated projects. We aim to improve the state of the art, and facilitate the open exchange of ideas and exchange of chemical data leveraging the best technologies ranging from quantum chemistry codes, molecular dynamics, informatics and visualization.

This repository contains git submodules for the Open Chemistry projects: Avogadro, MoleQueue and MongoChem. It can be used to download all relevant source files as well as building many of the necessary dependencies. Please see the documentation in the submodules for more details about each project.

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][Doxygen] with updated documentation generated nightly. We have several mailing lists to coordinate development and to provide support.

molequeue's People

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molequeue's Issues

Libraries with soname

Hi all.

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

Port to Qt6

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

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()

Failed version check for GCC 7

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

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

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

The "Queue and Program" list is empty.

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]

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.

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

Names should match, obviously.

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!

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)