- 08 Dec, 2022 6 commits
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Sandipan Mohanty authored
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Sandipan Mohanty authored
Depending on the TBB version found, we now use task_arena if available, or else, task_scheduler_init. This patch has the necessary changes to FindTBB.cmake and the CMakeLists.txt of the ParUtils library.
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Sandipan Mohanty authored
regularize, extract_props and multi_hist_cv can again use -threads option with TBB versions providing task_arena as well as older versions only providing task_scheduler_init.
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Sandipan Mohanty authored
Here we restore the -threads option for simulation programs like ParTempRun for recent TBB versions without task_scheduler_init. Like in the V210 branch, we use tbb::task_arena. But for V200, we want to preserve compatibility with older (pre-oneapi) versions of TBB. When such a TBB version is used, CMake has to find the old tbb::task_scheduler_init, and set up some compile definitions, like PRF_USE_TASK_SCHEDULER_INIT. The source files now check this macro to decide between task_scheduler_init and task_arena. Since these two ways to set up the number of workers differs in some significant ways, we end up with a some ugly pre-processor macros in the simulation programs.
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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- 06 Dec, 2022 8 commits
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
Recent versions of TBB (with OneAPI) have a header tbb/version.h with API version information. In older TBB versions we had a different header "tbb_stddef.h". ProFASi FindTBB.cmake looked for that older file. We could check for tbb/version.h, but that runs into complications that the file often has a single #include line including oneapi/version.h. This negates a simple filename switch. We therefore remove any checks based on tbb_stddef.h, so that ProFASi can compile when the version is recent enough. We lose descriptive error messages when the API version is too old though.
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
Some recent versions of tbb do not have tbb::task_scheduler_init. The current development branch of ProFASi uses the task arena to set up the tbb executor. Version 2.0 of ProFASi still used the task_scheduler_init for this purpose, and worked with older TBB versions. In order to maintain compatibility with versions of TBB with and without the task_scheduler_init, we make some features depend on the existence of task_scheduler_init. ProFASi will build and run fine without it, but some options, such as setting the thread count through command line options will not work. It would be possible to change this branch to task arena, but we will try to avoid doing so for this retiring branch.
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- 06 Dec, 2019 1 commit
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Sandipan Mohanty authored
When both comparison structures in RMSD come from the simulation, the RMSD value returned was incorrect, as it was still calculated on the assumption of fixedness of the first structure. Properties of the first structure such as radius of gyration, used in the RMSD calculation were calculated and stored at initialisation were used throughout, even when the first structure was not a fixed one from a PDB file.
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- 25 Oct, 2019 1 commit
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Jan Meinke authored
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- 24 Oct, 2019 1 commit
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Jan Meinke authored
The lines in the description of argparse are wrapped by default. Since we want to use the formatted doc string, we have to add `formatter_class=argparse.RawDescriptionHelpFormatter` as argument.
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- 17 Oct, 2019 9 commits
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Sandipan Mohanty authored
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Sandipan Mohanty authored
update_g, when called from ctest does not have an environment where other programs like "prf", "mc_stats" are in PATH. It therefore needs a special PATH set up for the subprocesses it spawns.
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Sandipan Mohanty authored
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Sandipan Mohanty authored
Live generation of gpars.out was broken, as pointed out by Stefan Wallin. The monte carlo statistics, such as visit counts to different temperatures are now calculated in bunches, and the counters are reset regularly. SimTempRun did not take that into account, and hence generated g_T = 0 for all T randomly in the middle of a run. The values in the file gpars.out were therefore completely wrong eversince the statistics collection method was changed. With this patch, we simply remove the live generation of gpars.out file, and move that action to a post processing step. The user is now supposed to run "prf simtemp update_g" after a simulated tempering run to generate a new g parameters file, and replace the gpars.in file consciously. There is more flexibility now, as we can choose how much of the previous run should be used to re-calculate the g-parameters after the run is finished and we have inspected the "rt" files. For instance, to use cycles starting from 200000 in the calculation of new g-parameters, we can now do this "prf simtemp update_g --starting_cycle 200000". See "prf simtemp update_g --help" for details.
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Sandipan Mohanty authored
It is possible to request xml output with -xml. It is possible to pick a specific child node in the information tree with a -get option, similar to how prfxml handles that option.
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Sandipan Mohanty authored
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Sandipan Mohanty authored
SimTemp will now write the g-parameters in the binary configuration files, so that the parameters used in the simulation will always be available for inspection along with the binary data. The values will be visible using the runinfo system : "prf runinfo -m"
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Sandipan Mohanty authored
If we try to open a normal file with JoinedTextFileIstream, it should emit an error, because all read operations will fail. For now, non-existent files are handled separately.
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Sandipan Mohanty authored
We expand the "prf" script interface to add a few scripts to manage simulated tempering runs. Eventually, there should be some setup scripts, and may be simulated tempering specific post-processing scripts here. For now, we have only the cover script "prf simtemp" and "prf simtemp update_g". The later calculates new g-parameters from input g-parameters and the visit counts to different temperatures collected from a run. This will now be the "official" way to update g-parameters. The parameters as generated during a run are no longer correct as they only take the visit counts in the latest "packet" in the monte carlo statistics. The live generation of gpars.out will be removed.
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- 24 Sep, 2019 1 commit
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Jan Meinke authored
The user documentation that was included in the source code of the corresponding classes was moved to reStructuredText files in the doc directory. It is now available again when documentation is build, but some cleanup is still needed.
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- 19 Sep, 2019 4 commits
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Sandipan Mohanty authored
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Sandipan Mohanty authored
Incremental update does not access elements of a zero sized array anymore ObsExpression initializes its internal copy of the incremental update. Observable gets new functions to getPopulation(), as that can be used to selectively and lazily initialize some.
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Sandipan Mohanty authored
When a new FF term is added after the force field has been fully set up, the newly added term must be given a population and initialized.
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Sandipan Mohanty authored
While harvesting possible disulphide bond sites, Seq(i) was previously compared with C. For proteins with an N-terminal ligand, Seq(i) would be offset by 1 compared to the index needed for accessing the i'th amino acid. It's better to compare AA(j)->OLC() with C. We also extend the search for the participating Sulfur atom to both the labels " SG " and "_SG_".
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- 18 Sep, 2019 2 commits
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Sandipan Mohanty authored
Some vestigial warning messages about the total number of moved atoms and apparent misplacement of atoms discovered during update_cells() were silenced.
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Sandipan Mohanty authored
A typo broke the message about the atoms involved in a disulphide bond, writing out the id of the first atom twice. A logical operator, which should have been "and" was mistakenly written as "or".
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- 16 Nov, 2018 7 commits
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
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Sandipan Mohanty authored
In prf::Wrap, because of copy-and-paste, post-increment and post-decrement operators were incorrectly returning references, leading to dangling references and SEGFAULTS.
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Sandipan Mohanty authored
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Sandipan Mohanty authored
GroupLibXML represents an XML node containing information about entities available for simulation, presumably provided by the force field class.
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