Build issues

[kyleabeauchamp]

This was reported by Nanjie Deng at Rutgers.

I am trying to use msmbuilder to construct a a MSM from a long CHARMM DCD file. But I am running into problems in installing MSMBuilder. The error occurs when some C library is compiled:

/usr/bin/ld: cannot find -lpython2.7 collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1

It seems that the library path for libpython2.7 needs to be in the compilation command. I use an Enthought (Canopy) python distribution, and the libpython2.7.so is located in ~/Enthought/Canopy_64bit/User/lib/.

But after some search, I cannot find where this gcc command is located in the downloaded MSMbuilder directory.

Could you tell me how to add the libpython2.7.so path to make the compilation work? May be I have missed some other necessary steps?

[rmcgibbo]

Nanjie,

Enthought canopy isn't installed correctly. In particular the dynamic linker isn't configured to find the libraries. If you're on mac, you might need to add

export DYLD_LIBRARY_PATH=$HOME/Enthought/Canopy_64bit/User/lib:$DYLD_LIBRARY_PATH

to your ~/.bashrc, and then restart your terminal.

On linux, the equivalent command is

export LD_LIBRARY_PATH=$HOME/Enthought/Canopy_64bit/User/lib:$LD_LIBRARY_PATH

[kyleabeauchamp]

Shouldn't numpy distutils automatically add the correct paths by inspecting the numpy builds? For some reason I thought that just "worked" without having explicit linker paths set? It certainly does on my machine...

[rmcgibbo]

The full printout of the the stdout and stderr from python setup.py install would be useful.

[nanjie]

Hi Kyle and Robert,

Thank you for the help. Yes, I tried adding $HOME/Enthought/Canopy_64bit/User/lib to LD_LIBRARY_PATH, but got the same error. The entire error message I got after python setup.py install --prefix=/home/ndeng/msm2.6.0 is copied below. Many thanks.

[ndeng@che-deng msmbuilder-2.6.0]$ python setup.py install --prefix=/home/ndeng/msm2.6.0 Appending msmbuilder.scripts configuration to msmbuilder Ignoring attempt to set 'name' (from 'msmbuilder' to 'msmbuilder.scripts') Appending msmbuilder.geometry configuration to msmbuilder Ignoring attempt to set 'name' (from 'msmbuilder' to 'msmbuilder.geometry') Appending msmbuilder.project configuration to msmbuilder Ignoring attempt to set 'name' (from 'msmbuilder' to 'msmbuilder.project') Appending msmbuilder.lumping configuration to msmbuilder Ignoring attempt to set 'name' (from 'msmbuilder' to 'msmbuilder.lumping') Appending msmbuilder.metrics configuration to msmbuilder Ignoring attempt to set 'name' (from 'msmbuilder' to 'msmbuilder.metrics') running install running bdist_egg running egg_info running build_src build_src building extension "msmbuilder._asa" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. building extension "msmbuilder.libxdrfile" sources building extension "msmbuilder.dcdplugin_s" sources building extension "msmbuilder._rmsdcalc" sources building extension "msmbuilder._distance_wrap" sources building extension "msmbuilder._dihedral_wrap" sources building extension "msmbuilder._contact_wrap" sources building extension "msmbuilder._rg_wrap" sources building data_files sources build_src: building npy-pkg config files writing requirements to msmbuilder.egg-info/requires.txt writing msmbuilder.egg-info/PKG-INFO writing top-level names to msmbuilder.egg-info/top_level.txt writing dependency_links to msmbuilder.egg-info/dependency_links.txt reading manifest file 'msmbuilder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README' warning: no files found matching 'RevisionHistory.txt' warning: no directories found matching 'TUTORIAL/xtc' warning: no directories found matching 'Docs' writing manifest file 'msmbuilder.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py copying src/python/version.py -> build/lib.linux-x86_64-2.7/msmbuilder running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'msmbuilder.dcdplugin_s' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -fPIC

creating build/temp.linux-x86_64-2.7/src/ext/molfile_plugin compile options: '-Isrc/ext/molfile_plugin/include/ -Isrc/ext/molfile_plugin -I/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/site-packages/numpy/core/include -I/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/include/python2.7 -c' gcc: src/ext/molfile_plugin/dcdplugin_s.c gcc -pthread -shared -g -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib -Wl,-rpath,'$ORIGIN/../lib' build/temp.linux-x86_64-2.7/src/ext/molfile_plugin/dcdplugin_s.o -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/msmbuilder/dcdplugin_s.so /usr/bin/ld: cannot find -lpython2.7 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lpython2.7 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared -g -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib -Wl,-rpath,'$ORIGIN/../lib' build/temp.linux-x86_64-2.7/src/ext/molfile_plugin/dcdplugin_s.o -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/msmbuilder/dcdplugin_s.so" failed with exit status 1

[rmcgibbo]

You've got like two python's installed ontop of each other or something? From the -L line, its trying to link against the python lib in /home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. I don't think that's what you want.

What happens when you type which python?

[nanjie]

Right. After I typed "which python", I got ~/Enthought/Canopy_64bit/User/bin/python, which seems to point to Enthought python.

But yes I also have a python at /usr/bin/python. Shall I uninstall and reinstall Enthought? Do I need root password to install Enthought?

Thanks a lot.

[rmcgibbo]

No, the issue is not the python at /usr/bin/python, it's the one in /home/builder/jenkins/workspace.

Can you also print the output of the following command?

python -c "import sys; print sys.path"

[nanjie]

Hi Robert,

I see, but I don't have this /home/builder/jenkins/workspace/... directory. I don't know how this long name enters the Msmbuilder system's makefile.

Nanjie

On Tue, Apr 23, 2013 at 3:06 PM, Robert McGibbon notifications@github.comwrote:

You've got like two python's installed ontop of each other or something? From the -L line, its trying to link against the python lib in /home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. I don't think that's what you want.

What happens when you type which python?

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16879443 .

[nanjie]

I got the following from "python -c "import sys; print sys.path":

['', '/home/ndeng/msm2.6.0/lib/python2.7/site-packages', '/net/briareus/u2/ndeng/projects/desres/msmbuild/msmbuilder-2.6.0', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python27.zip', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/plat-linux2', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/lib-tk', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/lib-old', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/lib-dynload', '/home/ndeng/Enthought/Canopy_64bit/User/lib/python2.7/site-packages', '/home/ndeng/Enthought/Canopy_64bit/System/lib/python2.7/site-packages', '/home/ndeng/Enthought/Canopy_64bit/System/lib/python2.7/site-packages/PIL', '/home/ndeng/Canopy/appdata/canopy-1.0.0.1160.rh5-x86_64/lib/python2.7/site-packages']

Is this correct?

[rmcgibbo]

Yeah, that looks fine. The third entry is probably not right, but it wouldn't be causing any harm.

I really don't know what's going on. Phenomenologically, what's happening is that you're trying to link against the wrong libpython.so. The proof is in the -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. But I don't know why that would be happening. If I were you, I might try grepping around for where that path is being written.

It could be an issue with ldconfig maybe. Perhaps sudo ldconfig could help. Or switching versions of python, either by reinstalling canopy, installing anaconda python (https://store.continuum.io/cshop/anaconda), installing from source (pretty easy on linux, this might help get you started) or trying to use your package manager's python (sudo apt-get install python-dev python-numpy python-tables should get you started).

[nanjie]

Thank you Robert. I will try the list of options you mentioned ans see how it goes. Best,

Nanjie

On Tue, Apr 23, 2013 at 3:31 PM, Robert McGibbon notifications@github.comwrote:

Yeah, that looks fine. The third entry is probably not right, but it wouldn't be causing any harm.

I really don't know what's going on. Phenomenologically, what's happening is that you're trying to link against the wrong libpython.so. The proof is in the -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. But I don't know why that would be happening. If I were you, I might try grepping around for where that path is being written.

It could be an issue with ldconfig maybe. Perhaps sudo ldconfig could help. Or switching versions of python, either by reinstalling canopy, installing anaconda python (https://store.continuum.io/cshop/anaconda), installing from source (pretty easy on linux, thishttps://gist.github.com/rmcgibbo/3433915might help get you started) or trying to use your package manager's python (sudo apt-get install python-dev python-numpy python-tables should get you started).

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16880871 .

[nanjie]

Hi Robert,

I found that this "-L/home/builder/jenkins/ workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib" resides in a Enthought code. I am convinced that it's my Enthought setup problem. I am wondering if you guys have used VirtualEnv to setup python package? Would VirtualEnv work with MSMBuilder?

Thanks,

Nanjie

On Tue, Apr 23, 2013 at 3:31 PM, Robert McGibbon notifications@github.comwrote:

Yeah, that looks fine. The third entry is probably not right, but it wouldn't be causing any harm.

I really don't know what's going on. Phenomenologically, what's happening is that you're trying to link against the wrong libpython.so. The proof is in the -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. But I don't know why that would be happening. If I were you, I might try grepping around for where that path is being written.

It could be an issue with ldconfig maybe. Perhaps sudo ldconfig could help. Or switching versions of python, either by reinstalling canopy, installing anaconda python (https://store.continuum.io/cshop/anaconda), installing from source (pretty easy on linux, thishttps://gist.github.com/rmcgibbo/3433915might help get you started) or trying to use your package manager's python (sudo apt-get install python-dev python-numpy python-tables should get you started).

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16880871 .

[kyleabeauchamp]

Hmm.

Maybe you should just try Anaconda? I can verify that my system builds with Anaconda (Ubuntu 12.10 64).

https://store.continuum.io/

[nanjie]

Thanks, yes, I will try Anaconda python. Will let you know.

Nanjie

On Tue, Apr 23, 2013 at 6:24 PM, kyleabeauchamp notifications@github.comwrote:

Hmm.

Maybe you should just try Anaconda? I can verify that my system builds with Anaconda (Ubuntu 12.10 64).

https://store.continuum.io/

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16890629 .

[kyleabeauchamp]

Be sure to get an Academic license--it allows you to use MKL and Accelerate, which could speed up your calculations.

[nanjie]

Got it, thank you Kyle!

On Tue, Apr 23, 2013 at 6:32 PM, kyleabeauchamp notifications@github.comwrote:

Be sure to get an Academic license--it allows you to use MKL and Accelerate, which could speed up your calculations.

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16891064 .

[rmcgibbo]

Yes, I use virtual env sometimes. I don't think that it will solve this problem though. Virtual env uses the same libpython shared object files (it uses an isolated site-packages)

-Robert Sent from my iPhone.

On Tue, Apr 23, 2013 at 3:22 PM, nanjie notifications@github.com wrote:

Hi Robert, I found that this "-L/home/builder/jenkins/ workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib" resides in a Enthought code. I am convinced that it's my Enthought setup problem. I am wondering if you guys have used VirtualEnv to setup python package? Would VirtualEnv work with MSMBuilder? Thanks, Nanjie On Tue, Apr 23, 2013 at 3:31 PM, Robert McGibbon notifications@github.comwrote:

Yeah, that looks fine. The third entry is probably not right, but it wouldn't be causing any harm.

I really don't know what's going on. Phenomenologically, what's happening is that you're trying to link against the wrong libpython.so. The proof is in the -L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib. But I don't know why that would be happening. If I were you, I might try grepping around for where that path is being written.

It could be an issue with ldconfig maybe. Perhaps sudo ldconfig could help. Or switching versions of python, either by reinstalling canopy, installing anaconda python (https://store.continuum.io/cshop/anaconda), installing from source (pretty easy on linux, thishttps://gist.github.com/rmcgibbo/3433915might help get you started) or trying to use your package manager's python (sudo apt-get install python-dev python-numpy python-tables should get you started).

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16880871 .

---

Reply to this email directly or view it on GitHub: https://github.com/SimTk/msmbuilder/issues/181#issuecomment-16890516

[nanjie]

I see, thank you.

Nanjie

On Tue, Apr 23, 2013 at 7:33 PM, Robert McGibbon notifications@github.comwrote:

Yes, I use virtual env sometimes. I don't think that it will solve this problem though. Virtual env uses the same libpython shared object files (it uses an isolated site-packages)

-Robert Sent from my iPhone.

On Tue, Apr 23, 2013 at 3:22 PM, nanjie notifications@github.com wrote:

Hi Robert, I found that this "-L/home/builder/jenkins/ workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib" resides in a Enthought code. I am convinced that it's my Enthought setup problem. I am wondering if you guys have used VirtualEnv to setup python package? Would VirtualEnv work with MSMBuilder? Thanks, Nanjie On Tue, Apr 23, 2013 at 3:31 PM, Robert McGibbon notifications@github.comwrote:

Yeah, that looks fine. The third entry is probably not right, but it wouldn't be causing any harm.

I really don't know what's going on. Phenomenologically, what's happening is that you're trying to link against the wrong libpython.so. The proof is in the

-L/home/builder/jenkins/workspace/Python_Masters/ARCH/x86_64/label/Linux/core/lib.

But I don't know why that would be happening. If I were you, I might try grepping around for where that path is being written.

It could be an issue with ldconfig maybe. Perhaps sudo ldconfig could help. Or switching versions of python, either by reinstalling canopy, installing anaconda python (https://store.continuum.io/cshop/anaconda),

installing from source (pretty easy on linux, this< https://gist.github.com/rmcgibbo/3433915>might help get you started) or trying to use your package manager's python (sudo apt-get install python-dev python-numpy python-tables should get you started).

— Reply to this email directly or view it on GitHub< https://github.com/SimTk/msmbuilder/issues/181#issuecomment-16880871> .

---

Reply to this email directly or view it on GitHub: https://github.com/SimTk/msmbuilder/issues/181#issuecomment-16890516

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16893750 .

[nanjie]

Hi Kyle,

The msmbuilder installation went much further with Anacoda python. But there is still an error about fastcluster algorithm, have you seen this before?

Nanjie

Installed /net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg Processing dependencies for msmbuilder==2.6.0 Searching for fastcluster Reading http://pypi.python.org/simple/fastcluster/ Reading http://math.stanford.edu/~muellner Reading http://math.stanford.edu/~muellner/fastcluster.html Best match: fastcluster 1.1.9 Downloading http://pypi.python.org/packages/source/f/fastcluster/fastcluster-1.1.9.tar.gz#md5=be5d7df51ee5c7ec6227368f46930b79 Processing fastcluster-1.1.9.tar.gz Writing /tmp/easy_install-xrbXDb/fastcluster-1.1.9/setup.cfg Running fastcluster-1.1.9/setup.py -q bdist_egg --dist-dir /tmp/easy_install-xrbXDb/fastcluster-1.1.9/egg-dist-tmp-MHw11G Version: 1.1.9 error: Setup script exited with error: SandboxViolation: os.open('/tmp/tmpeKQK9B/XBei8j', 131266, 384) {}

The package setup script has attempted to modify files on your system that are not within the EasyInstall build area, and has been aborted.

This package cannot be safely installed by EasyInstall, and may not support alternate installation locations even if you run its setup script by hand. Please inform the package's author and the EasyInstall maintainers to find out if a fix or workaround is available.

On Tue, Apr 23, 2013 at 6:32 PM, kyleabeauchamp notifications@github.comwrote:

Be sure to get an Academic license--it allows you to use MKL and Accelerate, which could speed up your calculations.

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16891064 .

[kyleabeauchamp]

Here's the download link to FastCluster. It appears that their package doesn't auto-download.

http://cran.r-project.org/web/packages/fastcluster/

[nanjie]

Thank you, Kyle. It's installed OK. Also have gone through alanine-dipeptide tutorial fine using XTC trajectories. But the run using DCD trajectories somehow failed, I will bother you if I can't figure out why.

[kyleabeauchamp]

Feel free to post the error message here.

[nanjie]

Hi, I got the following error when I type "ConvertDataToHDF.py -s native.pdb -i DCD -S file_dcd" to convert dcd files in the tutorial directory to HDF file.

{'input_dir': 'DCD', 'min_length': 0, 'pdb': 'native.pdb', 'project': 'ProjectInfo.yaml', 'quiet': False, 'rmsd_cutoff': -1, 'source': 'file_dcd', 'stride': 1} 17:06:00 - WARNING: Sorting trajectory files by numerical values in their names. 17:06:00 - Ensure that numbering is as intended. 17:06:00 - Found 100 traj dirs ['DCD/RUN00/frame0.dcd'] dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "/home/ndeng/msm2.6.0/bin/ConvertDataToHDF.py", line 5, in pkg_resources.run_script('msmbuilder==2.6.0', 'ConvertDataToHDF.py') File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 136, in args.min_length, args.stride, rmsd_cutoff) File "/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 70, in run pb.get_project().save(projectfn) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 128, in get_project self.convert() File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 159, in convert traj = self._load_traj(file_list) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 223, in _load_traj traj = Trajectory.load_from_dcd(file_list, PDBFilename=self.conf_filename) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 420, in load_from_dcd for c in dcd.DCDReader(FilenameList): File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/dcd.py", line 200, in next coords = np.asfarray(np.array(xyzvec).reshape(self.natoms.value, 3)) ValueError: total size of new array must be unchanged

[rmcgibbo]

Let's close this issue, and open up a new issue for the DCD reader.

-Robert

On 04/24/2013 02:09 PM, nanjie wrote:

Hi, I got the following error when I type "ConvertDataToHDF.py -s native.pdb -i DCD -S file_dcd" to convert dcd files in the tutorial directory to HDF file.

{'input_dir': 'DCD', 'min_length': 0, 'pdb': 'native.pdb', 'project': 'ProjectInfo.yaml', 'quiet': False, 'rmsd_cutoff': -1, 'source': 'file_dcd', 'stride': 1} 17:06:00 - WARNING: Sorting trajectory files by numerical values in their names. 17:06:00 - Ensure that numbering is as intended. 17:06:00 - Found 100 traj dirs ['DCD/RUN00/frame0.dcd'] dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "/home/ndeng/msm2.6.0/bin/ConvertDataToHDF.py", line 5, in pkg_resources.run_script('msmbuilder==2.6.0', 'ConvertDataToHDF.py') File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 136, in args.min_length, args.stride, rmsd_cutoff) File "/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py", line 70, in run pb.get_project().save(projectfn) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 128, in get_project self.convert() File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 159, in convert traj = self._load_traj(file_list) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py", line 223, in _load_traj traj = Trajectory.load_from_dcd(file_list, PDBFilename=self.conf_filename) File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 420, in load_from_dcd for c in dcd.DCDReader(FilenameList): File "/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/dcd.py", line 200, in next coords = np.asfarray(np.array(xyzvec).reshape(self.natoms.value, 3)) ValueError: total size of new array must be unchanged

— Reply to this email directly or view it on GitHub https://github.com/SimTk/msmbuilder/issues/181#issuecomment-16965468.

[nanjie]

Right. I just opened a new issue https://github.com/SimTk/msmbuilder/issues/183.

Nanjie

On Wed, Apr 24, 2013 at 5:14 PM, Robert McGibbon notifications@github.comwrote:

Let's close this issue, and open up a new issue for the DCD reader.

-Robert

On 04/24/2013 02:09 PM, nanjie wrote:

Hi, I got the following error when I type "ConvertDataToHDF.py -s native.pdb -i DCD -S file_dcd" to convert dcd files in the tutorial directory to HDF file.

{'input_dir': 'DCD', 'min_length': 0, 'pdb': 'native.pdb', 'project': 'ProjectInfo.yaml', 'quiet': False, 'rmsd_cutoff': -1, 'source': 'file_dcd', 'stride': 1} 17:06:00 - WARNING: Sorting trajectory files by numerical values in their names. 17:06:00 - Ensure that numbering is as intended. 17:06:00 - Found 100 traj dirs ['DCD/RUN00/frame0.dcd'] dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "/home/ndeng/msm2.6.0/bin/ConvertDataToHDF.py", line 5, in pkg_resources.run_script('msmbuilder==2.6.0', 'ConvertDataToHDF.py') File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/ndeng/anaconda/lib/python2.7/site-packages/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File

"/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py",

line 136, in args.min_length, args.stride, rmsd_cutoff) File

"/net/briareus/u2/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/ConvertDataToHDF.py",

line 70, in run pb.get_project().save(projectfn) File

"/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py",

line 128, in get_project self.convert() File

"/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py",

line 159, in convert traj = self._load_traj(file_list) File

"/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/project/builder.py",

line 223, in _load_traj traj = Trajectory.load_from_dcd(file_list, PDBFilename=self.conf_filename) File

"/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py",

line 420, in load_from_dcd for c in dcd.DCDReader(FilenameList): File

"/home/ndeng/msm2.6.0/lib/python2.7/site-packages/msmbuilder-2.6.0-py2.7-linux-x86_64.egg/msmbuilder/dcd.py",

line 200, in next coords = np.asfarray(np.array(xyzvec).reshape(self.natoms.value, 3)) ValueError: total size of new array must be unchanged

— Reply to this email directly or view it on GitHub https://github.com/SimTk/msmbuilder/issues/181#issuecomment-16965468.

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/181#issuecomment-16966139 .