Hi Geoff, On 19.06.2012 18:57, Geoffrey Hutchison wrote: >> I followed your advise. After editing the CMakeCache.txt and adding >> the >> compiler flags OpenMP is working for me. However, I would like to >> avoid >> this additional step by adding some conditional compilation lines to >> the >> CMakeLists.txt > > This seems reasonable, since OMP_NUM_THREADS is needed before the > OpenMP portion actually runs. >
In the email that I sent you, I explicitly declared how many cores to use by setting the OMP_NUM_THREADS variable in my environment. However the default behaviour for OpenMP is to use the maximum number of cores available (in case no OMP_NUM_THREADS is enabled and code has been compiled with OpenMP support and running in a multicore system with GOMP) So what I'm saying is that by adding those lines in CMakeLists.txt and suggesting users to install OpenMP in their multicore computers, they will benefit from multicore performance even if they don't set OMP_NUM_THREADS. >> I tried this lines with a fresh development version of OpenBabel and >> it >> seems to be working. I tried both having a setup with GOMP >> libraries >> installed and one without. I also run the ctest for MMFF94 just to >> be >> sure everything was working. > > Good, thanks. I'll try adding it to the SVN development code and we > can see how it does on the other test machines: > http://my.cdash.org/index.php?project=Open+Babel&display=project > Good thanks. I saw that you already added the lines and I also see the test failed for some of the test machines: http://my.cdash.org/testSummary.php?project=57&name=ffmmff94_Test&date=2012-06-20 However, I cannot see any particular information on why the test is failing. Anyway I saw one of the systems failing is a MacOS X running GCC. I will borrow a MAC laptop here at work and try to replicate this setting to find out if I can gain more insight. >> run two instances of OBForceFieldMMFF94 are being created. I would >> like >> to understand why is that, because I thought only one was necessary >> and >> therefore I am confused about this. > > I don't know. You'd need to run a debugger or something like Valgrind > to figure out what part of the code is creating each instance. In > this > particular code, only one instance should be created. > Yes. That's also what I thought and that's the reason why I asked you. I created an static variable in OBForceFieldMMFF94 to count how many times the class is being instantiated and I found it was two every time. Either when running obminimize or the ctest for mmff94. I will try the debugger and see if I can figure out what is going on. -- Omar V.M. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
