NameError: global name 'EMANVERSION' is not defined #137
Comments
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Hi Jianhao,
you reported a similar problem last month, and I suggested it was an issue with installing the CentOS7 version on a CentOS6 machine, then you said you tried a different computer and that machine was ok, and you never followed up on the original machine. The last time you reported the e2version.py output, which indicated this was the problem. This time you didn't include that.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell, Jr. Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem)
Co-Director CIBR Center (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu)
Baylor College of Medicine
sludtke@bcm.edu
On Oct 27, 2017, at 4:49 AM, jianhaoc ***@***.***> wrote:
Hi specialists,
I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.
$ e2display.py
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in
from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser
ImportError: cannot import name EMANVERSION
I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.
$ e2reliontoeman.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in
main()
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
$ e2proc2d.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in
main()
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
Am I missing something? Thank you!
Regards,
Jianhao
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Hi Steve Regards, For centos6 version For centos7 version for centos6 version $ e2reliontoeman.py --help $ e2proc3d.py --help Options: |
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@jianhaoc , you seem to be on CentOS6, so centos7 version, probably, won't run. When your centos6 installation is active, can you provide the output for the following? |
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Hi @shadowwalkersb , $ conda info -a conda environments:root * /home/jianhaoc/s/eman22centos6_20171028 sys.version: 2.7.13 | packaged by conda-forge | (defa... CIO_TEST: WARNING: could not import _license.show_info try:$ conda install -n root _license$ which -a e2proc2d.py $ e2proc2d.py --help positional arguments: optional arguments: $ e2reliontoeman.py --apix 2.5 --verbose 9 --refinedefocus p.star
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Hi Jianhao,
did we go through this once before? Maybe it was someone else... The error you are seeing there:
indicates that the disk you have your project on does not support file locking, which is critical to maintain file integrity. This usually happens with poorly configured remote filesystems, or external hard drives with old windows filesystems (not sure if this has that problem).
While shared filesystems can be fine when configured properly, in most cases they will be much slower than local storage (internal hard drive/RAID). External "portable" hard drives should never be used directly for data processing or as the only long term copy of your data, as their failure rate is MUCH higher than internal drives, they are even slower than remote filesystems in most cases, and (if they are USB) tend to have transitory I/O issues which can lead to jobs crashing. You may successfully get away with this approach for a while, but you are just asking for disaster.
Anyway, if this is your problem, I would strongly encourage you to copy your project onto internal storage on the computer and do your processing there, using the external drive or remote storage for backups.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell, Jr. Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu/>)
Baylor College of Medicine
sludtke@bcm.edu<mailto:sludtke@bcm.edu>
On Oct 31, 2017, at 3:20 AM, jianhaoc <notifications@github.com<mailto:notifications@github.com>> wrote:
Hi @shadowwalkersb<https://github.com/shadowwalkersb> ,
Please see below. Besides what you ask to do, I also tried e2reliontoeman.py. Thank you.
$ conda info -a
Current conda install:
platform : linux-64
conda version : 4.3.21
conda is private : False
conda-env version : 4.3.21
conda-build version : 2.1.15
python version : 2.7.13.final.0
requests version : 2.14.2
root environment : /home/jianhaoc/s/eman22centos6_20171028 (writable)
default environment : /home/jianhaoc/s/eman22centos6_20171028
envs directories : /home/jianhaoc/s/eman22centos6_20171028/envs
/home/jianhaoc/.conda/envs
package cache : /home/jianhaoc/s/eman22centos6_20171028/pkgs
/home/jianhaoc/.conda/pkgs
channel URLs : https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/linux-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
config file : /home/jianhaoc/.condarc
netrc file : None
offline mode : False
user-agent : conda/4.3.21 requests/2.14.2 CPython/2.7.13 Linux/2.6.32-573.12.1.el6_lustre.x86_64 CentOS/6.7 glibc/2.12
UID:GID : 1012:1012
conda environments:
root * /home/jianhaoc/s/eman22centos6_20171028
sys.version: 2.7.13 | packaged by conda-forge | (defa...
sys.prefix: /home/jianhaoc/s/eman22centos6_20171028
sys.executable: /home/jianhaoc/s/eman22centos6_20171028/bin/python
conda location: /home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/conda
conda-build: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-build
conda-convert: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-convert
conda-develop: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-develop
conda-env: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-env
conda-index: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-index
conda-inspect: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-inspect
conda-metapackage: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-metapackage
conda-render: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-render
conda-sign: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-sign
conda-skeleton: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-skeleton
conda-verify: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-verify
user site dirs:
CIO_TEST:
CONDA_DEFAULT_ENV:
CONDA_ENVS_PATH:
LD_LIBRARY_PATH: /home/programs/openmpi/lib:/home/programs/fltk/lib:/home/programs/fftw/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpfr-3.1.4/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpc-1.0.3/build/lib
PATH: /home/jianhaoc/s/eman22centos6_20171028/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/build/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build::/home/programs/tools:/home/jianhaoc/s/relion/build/bin:/home/programs/openmpi/bin:/usr/local/bin:/usr/local/sbin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/iperf3/bin:/usr/local/rrdtool/bin:/usr/local/ganglia/bin:/usr/local/ganglia/sbin
PYTHONHOME:
PYTHONPATH:
WARNING: could not import _license.show_info
try:
$ conda install -n root _license
$ which -a e2proc2d.py
~/s/eman22centos6_20171028/bin/e2proc2d.py
$ e2proc2d.py --help
usage: e2proc2d.py [options] ...
MRC stack files MUST use the .mrcs extension to be treated as a set of 2-D images (or you must
use one of the --threed* options)
If there is more than one input file, then outputfile is a pattern, where @
in the pattern is replaced by the input file base name (minus any extension).
Generic 2-D image processing and file format conversion program. Acts on stacks of 2-D images
(multiple images in one file). All EMAN2 recognized file formats accepted (see Wiki for list).
You can create a new 2-D or 3-D image from scratch instead of reading from a file by specifying
':<nx>:<ny>:<expression_in_x_y>' or ':<nx>:<ny>:<nz>:<expression_in_x_y_z>' as an input filename,
where 0 <= x < nx, 0 <= y < ny, 0 <= z < nz, and the expression can be just a number.
If performing certain operations which do not require an output file, specify "none" as the output file.
Examples:
convert IMAGIC format test.hed to HDF format:
e2proc2d.py test.hed test.hdf
convert all MRC format files in current directory to HDF format:
e2proc2d.py *.mrc @.hdf
convert a 'set' (.lst file) to an MRC stack file:
e2proc2d.py sets/myset.lst myset.mrcs
create a new image, initialized with 1.0, then mask it:
e2proc2d.py :128:128:1 mymask.hdf --process mask.soft:outer_radius=50
apply a 10 A low-pass filter to a stack of particles downsample the particles by a factor of 2
and write output to a new file.
e2proc2d.py ptcl.hdf ptcl.filt.hdf --process filter.lowpass.gauss:cutoff_freq=0.1 --meanshrink 2
'e2help.py processors -v 2' for a detailed list of available procesors
positional arguments:
postionalargs
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--apix APIX A/pixel for S scaling
--average Averages all input images (without alignment) and
writes a single output image
--averager AVERAGER If --average is specified, this is the averager to use
(e2help.py averager). Default=mean
--calcsf outputfile calculate a radial structure factor for the image and
write it to the output file, must specify apix. divide
into angular bins
--calccont Compute the low resolution azimuthal contrast of each
image and put it in the header as
eval_contrast_lowres. Larger values imply more
'interesting' images.
--clip xsize,ysize Specify the output size in pixels
xsize,ysize[,xcenter,ycenter], images can be made
larger or smaller.
--exclude exclude-list-file
Excludes image numbers in EXCLUDE file
--fftavg filename Incoherent Fourier average of all images and write a
single power spectrum image
--process processor_name:param1=value1:param2=value2
apply a processor named 'processorname' with all its
parameters/values.
--mult k Multiply image by a constant. mult=-1 to invert
contrast.
--add f Adds a constant 'f' to the densities
--addfile ADDFILE Adds the volume to another volume of identical size
--first n the first image in the input to process [0 - n-1])
--last n the last image in the input to process
--list listfile Works only on the image numbers in LIST file
--select selectname Works only on the images in named selection set from
bdb:select
--inplace Output overwrites input, USE SAME FILENAME, DO NOT
'clip' images.
--interlv interleave-file
Specifies a 2nd input file. Output will be 2 files
interleaved.
--extractboxes Extracts box locations from the image header to
produce a set of .box files for only the particles in
the .lst files
--meanshrink n Reduce an image size by an integral (1.5 also allowed)
scaling factor using average. eg - 2 will reduce image
size to 1/2. Clip is not required.
--medianshrink n Reduce an image size by an integral scaling factor,
uses median filter. eg - 2 will reduce image size to
1/2. Clip is not required.
--fouriershrink n Reduce an image size by an arbitrary scaling factor by
clipping in Fourier space. eg - 2 will reduce image
size to 1/2.
--mraprep this is an experimental option
--outmode OUTMODE All EMAN2 programs write images with 4-byte floating
point values when possible by default. This allows
specifying an alternate format when supported (float,
int8, int16, int32, uint8, uint16, uint32). Values are
rescaled to fill MIN-MAX range.
--outnorescale If specified, floating point values will not be
rescaled when writing data as integers. Values outside
of range are truncated.
--mrc16bit (deprecated, use --outmode instead) output as 16 bit
MRC file
--mrc8bit (deprecated, use --outmode instead) output as 8 bit
MRC file
--fixintscaling FIXINTSCALING
When writing to an 8 or 16 bit integer format the data
must be scaled. 'noscale' will assume the pixel values
are already correct, 'sane' will pick a good range, a
number will set the range to mean+=sigmanumber
--multfile MULTFILE Multiplies the volume by another volume of identical
size. This can be used to apply masks, etc.
--norefs Skip any input images which are marked as references
(usually used with classes.)
--outtype image-type output image format, 'mrc', 'imagic', 'hdf', etc. if
specify spidersingle will output single 2D image
rather than 2D stack.
--radon Do Radon transform
--randomize RANDOMIZE
Randomly rotate/translate the image. Specify:
da,dxy,flip da is a uniform distribution over +-da
degrees, dxy is a uniform distribution on x/y, if flip
is 1, random handedness changes will occur
--rotavg Compute the 1-D rotational average of each image as a
final step before writing the output
--rotate ROTATE Rotate clockwise (in degrees)
--rfp this is an experimental option
--fp FP This generates rotational/translational 'footprints'
for each input particle, the number indicates which
algorithm to use (0-6)
--scale f Scale by specified scaling factor. Clip must also be
specified to change the dimensions of the output map.
--anisotropic ANISOTROPIC
Anisotropic scaling, stretches on one axis and
compresses the orthogonal axis. Specify amount,angle.
See e2evalrefine
--selfcl steps mode steps mode
Output file will be a 180x180 self-common lines map
for each image.
--setsfpairs Applies the radial structure factor of the 1st image
to the 2nd, the 3rd to the 4th, etc
--split n Splits the input file into a set of n output files
--translate TRANSLATE
Translate by x,y pixels
--headertransform HEADERTRANSFORM
This will take the xform.align2d header value from
each particle, and apply it. Pass 0 to perform the
transform or 1 to perform the inverse.
--verbose n, -v n verbose level [0-9], higner number means higher level
of verboseness
--plane ['xy', 'yx', 'xz', 'zx', 'yz', 'yz']
Change the plane of image processing, useful for
processing 3D mrcs as 2D images.
--writejunk Writes the image even if its sigma is 0.
--swap Swap the byte order
--threed2threed Process 3D image as a stack of 2D slices, then output
as a 3D image
--threed2twod Process 3D image as a stack of 2D slices, then output
as a 2D stack
--twod2threed Process a stack of 2D images, then output as a 3D
image.
--unstacking Process a stack of 2D images, then output a a series
of numbered single image files
--ppid PPID Set the PID of the parent process, used for cross
platform PPID
--step STEP Specify ,. Processes only a subset of the
input data. For example, 0,2 would process only the
even numbered particles
--parallel PARALLEL, -P PARALLEL
Run in parallel, specify type:n=:option:option
$ e2reliontoeman.py --apix 2.5 --verbose 9 --refinedefocus p.star
Parsing STAR file
Traceback (most recent call last):
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 567, in open_db
try : ret=JSDict(path)
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 638, in init
self.sync()
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 689, in sync
file_lock(jfile,readonly=False)
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 210, in file_lock
else : fcntl.lockf(fileobj.fileno(),fcntl.LOCK_EX)
IOError: [Errno 38] Function not implemented
Traceback (most recent call last):
File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 157, in
main()
File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 93, in main
prj=js_open_dict("info/project.json")
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 73, in js_open_dict
return JSDict.open_db(url)
File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 572, in open_db
raise Exception,"Unable to open "+path
Exception: Unable to open info/project.json
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--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell, Jr. Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu>)
Baylor College of Medicine
sludtke@bcm.edu<mailto:sludtke@bcm.edu>
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Hi @sludtke42 , |
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EMAN does support shared filesystems IF they are properly configured to support file locking. This does exclude certain types of old filesystems which don't support this concept at all.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell, Jr. Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu/>)
Baylor College of Medicine
sludtke@bcm.edu<mailto:sludtke@bcm.edu>
On Nov 1, 2017, at 9:22 AM, jianhaoc <notifications@github.com<mailto:notifications@github.com>> wrote:
Hi @sludtke42<https://github.com/sludtke42> ,
Thank you for reminding me about that. Because I cann't access to the EMAN googlegroup these days to find my question back, I asked it again here. What a pity the shared filesystems are unavailable for EMAN2.
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--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell, Jr. Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu>)
Baylor College of Medicine
sludtke@bcm.edu<mailto:sludtke@bcm.edu>
|
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Sorry for missing your meaning again. I meant my filesystem might be not setup properly. |
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Is there anything else to do here? Can this issue be closed? |
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Hi,
I turned to another computer without shared filesystems.
regards,
Jianhao
2018-05-01 6:13 GMT+08:00 shadow_walker <notifications@github.com>:
… Is there anything else to do here? Can this issue be closed?
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<#137 (comment)>, or mute
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Hi specialists,
I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.
$ e2display.py
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in
from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser
ImportError: cannot import name EMANVERSION
I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.
$ e2reliontoeman.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in
main()
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
$ e2proc2d.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in
main()
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
Am I missing something? Thank you!
Regards,
Jianhao
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