Comments (13)
Eigenstate
commented on July 17, 2024
I don't have access to an OSX machine so it may be a little annoying to debug this but I think I know how to fix things if I have some more info.
Is /usr/local/opt/python3/3.6/lib/libtcl8.5.dylib a file? Is it somewhere else, maybe /usr/lib?
Is it libtcl8.6.dylib instead?
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RasmusFonseca
commented on July 17, 2024
Ah yeah that'd be annoying. Ill be happy to come by in person. To answer your question:
$ find /usr/lib -name "libtcl*"
/usr/lib/libtcl.dylib
/usr/lib/libtcl8.5.dylib
/usr/lib/libtclstub8.5.afrom vmd-python.
RasmusFonseca
commented on July 17, 2024
Theres also
/usr/local/Cellar/tcl-tk/8.6.4/lib/libtcl8.6.dylib
/usr/local/Cellar/tcl-tk/8.6.4/lib/libtclstub8.6.a
/usr/local/Cellar/tcl-tk/8.6.7/lib/libtcl8.6.dylib
/usr/local/Cellar/tcl-tk/8.6.7/lib/libtclstub8.6.a
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Eigenstate
commented on July 17, 2024
I'm actually out of town... but we can still figure it out.
is $DYLD_LIBRARY_PATH set to anything?
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RasmusFonseca
commented on July 17, 2024
Nothing that points to subdirs of /usr (just intel compiler stuff).
$ echo $DYLD_LIBRARY_PATH | tr ':' '\n'
/opt/intel//compilers_and_libraries_2016.2.146/mac/compiler/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/compiler/lib/intel64
/opt/intel//compilers_and_libraries_2016.2.146/mac/ipp/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/compiler/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/mkl/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/tbb/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/daal/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/daal/../tbb/lib
/opt/intel//compilers_and_libraries_2016.2.146/mac/daal/../compiler/libfrom vmd-python.
Eigenstate
commented on July 17, 2024
Try cloning this repo and building again. I think b7ec401 should fix it-- the installer wasn't looking in all the relevant places for the library.
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RasmusFonseca
commented on July 17, 2024
Would this relate to a pip install? I'm not sure how to point pip to a particular commit.
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Eigenstate
commented on July 17, 2024
Oh, I meant this repo.
git clone https://github.com/Eigenstate/vmd-python.git
cd vmd-python
python setup.py install
I also updated the anaconda installer so pip install should have that commit. The version string should be 2.0.5.
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RasmusFonseca
commented on July 17, 2024
Hm. I'm getting roughly the same error:
DN525uqm:~/Programs $ rm -rf vmd-python/
DN525uqm:~/Programs $ git clone https://github.com/Eigenstate/vmd-python.git
Cloning into 'vmd-python'...
remote: Counting objects: 7121, done.
remote: Compressing objects: 100% (35/35), done.
remote: Total 7121 (delta 33), reused 48 (delta 23), pack-reused 7063
Receiving objects: 100% (7121/7121), 38.29 MiB | 8.43 MiB/s, done.
Resolving deltas: 100% (2199/2199), done.
DN525uqm:~/Programs $ cd vmd-python
DN525uqm:~/Programs/vmd-python $ python3.6 setup.py install
/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'extras_require'
warnings.warn(msg)
running install
running build
Compiling VMD
Finding libraries...
Traceback (most recent call last):
File "setup.py", line 293, in <module>
'test': VMDTest,
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "setup.py", line 30, in run
self.execute(self.compile, [], msg="Compiling VMD")
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 335, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/util.py", line 301, in execute
func(*args)
File "setup.py", line 43, in compile
self.set_environment_variables(pydir)
File "setup.py", line 183, in set_environment_variables
fallback=False)
File "setup.py", line 141, in _find_library_dir
+ os.environ.get("DYLD_FALLBACK_LIBRARY_PATH").split(":")
AttributeError: 'NoneType' object has no attribute 'split'
DN525uqm:~/Programs/vmd-python $ pip install -i https://pypi.anaconda.org/rbetz/simple vmd-python
Collecting vmd-python
Downloading https://pypi.anaconda.org/rbetz/simple/vmd-python/2.0.5/vmd-python-2.0.5.tar.gz (27.8MB)
100% |████████████████████████████████| 27.8MB 67kB/s
Building wheels for collected packages: vmd-python
Running setup.py bdist_wheel for vmd-python ... error
Complete output from command /Users/rfonseca/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/tmppgyyv9r0pip-wheel- --python-tag cp36:
running bdist_wheel
running build
Compiling VMD
Finding libraries...
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 293, in <module>
'test': VMDTest,
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/Users/rfonseca/anaconda3/lib/python3.6/site-packages/wheel/bdist_wheel.py", line 179, in run
self.run_command('build')
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 30, in run
self.execute(self.compile, [], msg="Compiling VMD")
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 335, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/util.py", line 301, in execute
func(*args)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 43, in compile
self.set_environment_variables(pydir)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 183, in set_environment_variables
fallback=False)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 141, in _find_library_dir
+ os.environ.get("DYLD_FALLBACK_LIBRARY_PATH").split(":")
AttributeError: 'NoneType' object has no attribute 'split'
----------------------------------------
Failed building wheel for vmd-python
Running setup.py clean for vmd-python
Failed to build vmd-python
Installing collected packages: vmd-python
Running setup.py install for vmd-python ... error
Complete output from command /Users/rfonseca/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-_1r3mvr5-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
Compiling VMD
Finding libraries...
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 293, in <module>
'test': VMDTest,
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/Users/rfonseca/anaconda3/lib/python3.6/site-packages/setuptools/command/install.py", line 61, in run
return orig.install.run(self)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 30, in run
self.execute(self.compile, [], msg="Compiling VMD")
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 335, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/util.py", line 301, in execute
func(*args)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 43, in compile
self.set_environment_variables(pydir)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 183, in set_environment_variables
fallback=False)
File "/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py", line 141, in _find_library_dir
+ os.environ.get("DYLD_FALLBACK_LIBRARY_PATH").split(":")
AttributeError: 'NoneType' object has no attribute 'split'
----------------------------------------
Command "/Users/rfonseca/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-_1r3mvr5-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/pm/vtj2fdz94xxfw2sr59lsyrw40000gn/T/pip-build-t6gu3o10/vmd-python/from vmd-python.
Eigenstate
commented on July 17, 2024
Oops, I had a dumb mistake in there, fixed with df505fc. Git pull and try again? It'll still be 2.0.5
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RasmusFonseca
commented on July 17, 2024
Some progress .. new error 😀
DN525uqm:~/Programs/vmd-python $ git pull
remote: Counting objects: 3, done.
remote: Compressing objects: 100% (1/1), done.
remote: Total 3 (delta 2), reused 3 (delta 2), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/Eigenstate/vmd-python
359ef40..df505fc master -> origin/master
Updating 359ef40..df505fc
Fast-forward
setup.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
DN525uqm:~/Programs/vmd-python $ python3.6 setup.py install
/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'extras_require'
warnings.warn(msg)
running install
running build
Compiling VMD
Finding libraries...
Traceback (most recent call last):
File "setup.py", line 293, in <module>
'test': VMDTest,
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "setup.py", line 30, in run
self.execute(self.compile, [], msg="Compiling VMD")
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/cmd.py", line 335, in execute
util.execute(func, args, msg, dry_run=self.dry_run)
File "/Users/rfonseca/anaconda3/lib/python3.6/distutils/util.py", line 301, in execute
func(*args)
File "setup.py", line 43, in compile
self.set_environment_variables(pydir)
File "setup.py", line 183, in set_environment_variables
fallback=False)
File "/Users/rfonseca/anaconda3/lib/python3.6/os.py", line 674, in __setitem__
value = self.encodevalue(value)
File "/Users/rfonseca/anaconda3/lib/python3.6/os.py", line 744, in encode
raise TypeError("str expected, not %s" % type(value).__name__)
TypeError: str expected, not NoneType
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Eigenstate
commented on July 17, 2024
Hmmm that means it's still not finding libtcl in the right spot. Try it again?
git pull
python setup.py build
python setup.py install
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RasmusFonseca
commented on July 17, 2024
Finally back. It works now!
For the record, my python installation is through anaconda3 and I had to run brew install netcdf first.
Thank you
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Related Issues (20)
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