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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
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the problem about running Cluster.py #191

Closed smileyujun closed 11 years ago

smileyujun commented 11 years ago

Hi When i run :Cluster.py dihedral hybrid -k 100, it appears the fllowing fault :

[root@localhost hil-21-3a3]# Cluster.py dihedral hybrid -k 100

MSMBuilder version 2.6.0.dev-Unknown

See file AUTHORS for a list of MSMBuilder contributors.

Copyright 2011 Stanford University. MSMBuilder comes with ABSOLUTELY NO WARRANTY. MSMBuilder is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2

of the License, or (at your option) any later version.

Please cite the following references: GR Bowman, X Huang, and VS Pande. Methods 2009. Using generalized ensemble simulations and Markov state models to identify conformational states. KA Beauchamp, GR Bowman, TJ Lane, L Maibaum, IS Haque, VS Pande. JCTC 2011. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Timescale IS Haque, KA Beauchamp, VS Pande. In preparation. A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD. --------------------------------------------------------------------------------{'alg': 'hybrid', 'dihedral_angles': 'phi/psi', 'dihedral_metric': 'euclidean', 'dihedral_p': 2, 'hybrid_distance_cutoff': None, 'hybrid_global_iters': 0, 'hybrid_ignore_max_objective': False, 'hybrid_local_num_iters': 10, 'hybrid_num_clusters': 100, 'hybrid_too_close_cutoff': 0.0001, 'metric': 'dihedral', 'output_dir': 'Data/', 'project': 'ProjectInfo.yaml', 'quiet': False, 'stride': 1} 11:52:38 - Creating directory Data 11:52:50 - Loaded 1 trajs Traceback (most recent call last): File "/usr/local/bin/Cluster.py", line 5, in pkg_resources.run_script('msmbuilder==2.6.0', 'Cluster.py') File "/usr/local/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/lib/python2.7/site-packages/distribute-0.6.36-py2.7.egg/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/EGG-INFO/scripts/Cluster.py", line 228, in main(args, metric) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/EGG-INFO/scripts/Cluster.py", line 206, in main clusterer = cluster(metric, trajs, args, extra_kwargs) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/EGG-INFO/scripts/Cluster.py", line 141, in cluster ignore_max_objective=args.hybrid_ignore_max_objective) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/msmbuilder/clustering.py", line 1173, in init super(HybridKMedoids, self).init(metric, trajectories) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/msmbuilder/clustering.py", line 884, in init** self.ptraj = metric.prepare_trajectory(self._concatenated) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/msmbuilder/metrics/dihedral.py", line 94, in prepare_trajectory dihedrals = _dihedralcalc.compute_dihedrals(trajectory, indices, degrees=False) File "/usr/local/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-i686.egg/msmbuilder/geometry/dihedral.py", line 86, in compute_dihedrals xyzlist = np.array(xyzlist, dtype=np.float32, order='C') MemoryError [root@localhost hil-21-3a3]#

Where is my fault? Can you help me?

Yours sinerely

yujun zhou

kyleabeauchamp commented 11 years ago

It looks like you're running out of memory--your trajectory is too big to fit in RAM.

kyleabeauchamp commented 11 years ago

If your trajectory has solvent (water) coordinates, you might try remove those before your analysis. Otherwise, you can try subsampling the trajectory.

smileyujun commented 11 years ago

It hasn't solvent (water) coordinates, but my .xtc file(generated by Gromacs) is very big(about 257M in RAM),so the trajectory(generated by ConvertDataToHDF.py command) is very big(about 370M in RAM).

Then, how can i make it smaller in order to run MSMBuilder normally?

在 2013-05-09 12:40:55，kyleabeauchamp notifications@github.com 写道：

It looks like you're running out of memory--your trajectory is too big to fit in RAM.

— Reply to this email directly or view it on GitHub.

kyleabeauchamp commented 11 years ago

How much memory does your system have? Most modern systems have ~16GB or more, so 300M should not be a problem.

rmcgibbo commented 11 years ago

Well how much RAM do you have on your machine? You could perhaps do your analysis on a machine with more RAM.

Alternatively, try using the --stride flag for Cluster.py. If you run Cluster.py -h, you can see all of the options.

-Robert

On May 8, 2013, at 11:37 PM, smileyujun wrote:

It hasn't solvent (water) coordinates, but my .xtc file(generated by Gromacs) is very big(about 257M in RAM),so the trajectory(generated by ConvertDataToHDF.py command) is very big(about 370M in RAM).

Then, how can i make it smaller in order to run MSMBuilder normally?

在 2013-05-09 12:40:55，kyleabeauchamp notifications@github.com 写道：

It looks like you're running out of memory--your trajectory is too big to fit in RAM.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

smileyujun commented 11 years ago

My system has about 20GB memory , well, i will try it again.

At 2013-05-09 14:37:14,"玉君" smileyujunz@163.com wrote: It hasn't solvent (water) coordinates, but my .xtc file(generated by Gromacs) is very big(about 257M in RAM),so the trajectory(generated by ConvertDataToHDF.py command) is very big(about 370M in RAM).

Then, how can i make it smaller in order to run MSMBuilder normally?

在 2013-05-09 12:40:55，kyleabeauchamp notifications@github.com 写道：

It looks like you're running out of memory--your trajectory is too big to fit in RAM.

— Reply to this email directly or view it on GitHub.

smileyujun commented 11 years ago

Thanks very much, this problem has solved. But, the next problem appears. In the MSMBuilder 2.5 Tutorial, in the 4.2.8 chapter:Examining the macrostate decomposition

It is known that the relevant degrees of freedom for alanine dipeptide are the phi and psi backbone angles. Thus, it is useful to examine (phi,psi), which we have pre-calculated for you.

python PlotDihedrals.py Macro4/MacroAssignments.h5

After reading the above, i have the folowing confusions:

  1. What's the use of the phi and psi?(In the PlotDihedrals.py script,there are the phi and psi needed)
  2. When i run 'python PlotDihedrals.py Macro4/MacroAssignments.h5' command, What kind of files i need to ready?
  3. How can i modify the PlotDihedrals.py script for running my project normally?
smileyujun commented 11 years ago

In the MSMBuilder 2.5 Tutorial, in the 4.2.8 chapter:Examining the macrostate decomposition

It is known that the relevant degrees of freedom for alanine dipeptide are the phi and psi backbone angles. Thus, it is useful to examine (phi,psi), which we have pre-calculated for you.

python PlotDihedrals.py Macro4/MacroAssignments.h5

After reading the above, i have the folowing confusions:

  1. What's the use of the phi and psi?(In the PlotDihedrals.py script,there are the phi and psi needed)
  2. When i run 'python PlotDihedrals.py Macro4/MacroAssignments.h5' command, What kind of files i need to ready?
  3. How can i modify the PlotDihedrals.py script for running my project normally?
  4. When i run my protein, could i still use the phi and psi file provided by the tutorial? If the phi and psi files are needed, how can i open and modify them?

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rmcgibbo commented 11 years ago

The ala2 dihedrals are purely for visualization of that toy system. It is not applicable to a real protein, because real proteins are not adequately described by only two degrees of freedom.

smileyujun commented 11 years ago

Thankes for your reply. Recently, i'm doing my protein by MSMBuilder 2.5. In my protein, there are 5567 atoms, my protein is a protein-protein compound.

When i run 'GetRandomConfs.py -c 1 -f pdb' command, it oppears the following fault:

[cuiyf@localhost hil-21-2p2]$ GetRandomConfs.py -c 1 -f pdb

MSMBuilder version 2.5.1

See file AUTHORS for a list of MSMBuilder contributors.

Copyright 2011 Stanford University. MSMBuilder comes with ABSOLUTELY NO WARRANTY. MSMBuilder is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2

of the License, or (at your option) any later version.

Please cite the following references: GR Bowman, X Huang, and VS Pande. Methods 2009. Using generalized ensemble simulations and Markov state models to identify conformational states. KA Beauchamp, GR Bowman, TJ Lane, L Maibaum, IS Haque, VS Pande. JCTC 2011. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Timescale IS Haque, KA Beauchamp, VS Pande. In preparation. A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD. --------------------------------------------------------------------------------Pulling 1 for each of 99 Getting Conformations For state 0 Getting Conformations For state 1 Getting Conformations For state 2 Getting Conformations For state 3 Getting Conformations For state 4 Getting Conformations For state 5 Getting Conformations For state 6 Getting Conformations For state 7 Getting Conformations For state 8 Getting Conformations For state 9 Getting Conformations For state 10 Getting Conformations For state 11 Getting Conformations For state 12 Getting Conformations For state 13 Getting Conformations For state 14 Getting Conformations For state 15 Getting Conformations For state 16 Getting Conformations For state 17 Getting Conformations For state 18 Getting Conformations For state 19 Getting Conformations For state 20 Getting Conformations For state 21 Getting Conformations For state 22 Getting Conformations For state 23 Getting Conformations For state 24 Getting Conformations For state 25 Getting Conformations For state 26 Getting Conformations For state 27 Getting Conformations For state 28 Getting Conformations For state 29 Getting Conformations For state 30 Getting Conformations For state 31 Getting Conformations For state 32 Getting Conformations For state 33 Getting Conformations For state 34 Getting Conformations For state 35 Getting Conformations For state 36 Getting Conformations For state 37 Getting Conformations For state 38 Getting Conformations For state 39 Getting Conformations For state 40 Getting Conformations For state 41 Getting Conformations For state 42 Getting Conformations For state 43 Getting Conformations For state 44 Getting Conformations For state 45 Getting Conformations For state 46 Getting Conformations For state 47 Getting Conformations For state 48 Getting Conformations For state 49 Getting Conformations For state 50 Getting Conformations For state 51 Getting Conformations For state 52 Getting Conformations For state 53 Getting Conformations For state 54 Getting Conformations For state 55 Getting Conformations For state 56 Getting Conformations For state 57 Getting Conformations For state 58 Getting Conformations For state 59 Getting Conformations For state 60 Getting Conformations For state 61 Getting Conformations For state 62 Getting Conformations For state 63 Getting Conformations For state 64 Getting Conformations For state 65 Getting Conformations For state 66 Getting Conformations For state 67 Getting Conformations For state 68 Getting Conformations For state 69 Getting Conformations For state 70 Getting Conformations For state 71 Getting Conformations For state 72 Getting Conformations For state 73 Getting Conformations For state 74 Getting Conformations For state 75 Getting Conformations For state 76 Getting Conformations For state 77 Getting Conformations For state 78 Getting Conformations For state 79 Getting Conformations For state 80 Getting Conformations For state 81 Getting Conformations For state 82 Getting Conformations For state 83 Getting Conformations For state 84 Getting Conformations For state 85 Getting Conformations For state 86 Getting Conformations For state 87 Getting Conformations For state 88 Getting Conformations For state 89 Getting Conformations For state 90 Getting Conformations For state 91 Getting Conformations For state 92 Getting Conformations For state 93 Getting Conformations For state 94 Getting Conformations For state 95 Getting Conformations For state 96 Getting Conformations For state 97 Getting Conformations For state 98 Traceback (most recent call last): File "/usr/local/bin/GetRandomConfs.py", line 71, in args.output, args.format) File "/usr/local/bin/GetRandomConfs.py", line 34, in run random_confs.SaveToPDB(output) File "/usr/local/lib/python2.7/site-packages/msmbuilder/Trajectory.py", line 217, in SaveToPDB PDB.WritePDBConformation(Filename,self["AtomID"], self["AtomNames"],self["ResidueNames"],self["ResidueID"],self["XYZList"][i],self["ChainID"]) File "/usr/local/lib/python2.7/site-packages/msmbuilder/PDB.py", line 2602, in WritePDBConformation x=10*XYZ[i][0] IndexError: index 3610 is out of bounds for axis 0 with size 3610 [cuiyf@localhost hil-21-2p2] #

Meanwhile, My trajectory is right,it is generated by Gromacs. Where is my wrong ? How can i solve this problem?

静如处子，动若脱兔！

At 2013-05-10 15:57:32,"Robert McGibbon" notifications@github.com wrote:

The ala2 dihedrals are purely for visualization of that toy system. It is not applicable to a real protein, because real proteins are not adequately described by only two degrees of freedom.

— Reply to this email directly or view it on GitHub.