Relion 5 to eman2 + float16 mrcs files
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Matthew Belousoff
Nov 30, 2023, 9:05:30 PM11/30/23
to EMAN2
So I'm really keen to try out the new GMM refinement, but thought to test it out on a recently processed dataset from RELION. So instead of starting fresh in EMAN I wanted to convert the run_data.star and press on directly in EMAN2.
A few details first.
e2version.py
EMAN 2.99.54 ( GITHUB: 2023-12-01 10:48 - commit: 4e38f2525 )
Your EMAN2 is running on: Linux-5.15.0-89-generic-x86_64-with-glibc2.35 5.15.0-89-generic
Your Python version is: 3.11.6
Your Python version is: 3.11.6
When I run e3relion_convert.py (no matter what relative path in the RELION project) I get presented with the following error after it has finished parsing the STAR file:
Parsing STAR file
WARNING: Multiple optics groups detected in star file. EMAN3 does not support this at present. The first optics group will be used for all data, which may be incorrect.
Using rlnDefocusU to group particles into 30128 groups
WARNING: Unable to group particles usefully by micrograph, collapsing to a single file. Consider rerunning with sufficiently large --dftolerance
Traceback (most recent call last):
File "/home/mbelouso/anaconda3/envs/eman2/bin/e3relion_convert.py", line 249, in <module>
main()
File "/home/mbelouso/anaconda3/envs/eman2/bin/e3relion_convert.py", line 214, in main
img=EMData("../"+imfsp,imn-1) # relion starts with #1, EMAN #0
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN3.py", line 2910, in db_emd_init
self.read_image(*parms)
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN3.py", line 2983, in db_read_image
return self.read_image_c(fsp, *parms, **kparms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xbd in position 2: invalid start byte
WARNING: Multiple optics groups detected in star file. EMAN3 does not support this at present. The first optics group will be used for all data, which may be incorrect.
Using rlnDefocusU to group particles into 30128 groups
WARNING: Unable to group particles usefully by micrograph, collapsing to a single file. Consider rerunning with sufficiently large --dftolerance
Traceback (most recent call last):
File "/home/mbelouso/anaconda3/envs/eman2/bin/e3relion_convert.py", line 249, in <module>
main()
File "/home/mbelouso/anaconda3/envs/eman2/bin/e3relion_convert.py", line 214, in main
img=EMData("../"+imfsp,imn-1) # relion starts with #1, EMAN #0
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN3.py", line 2910, in db_emd_init
self.read_image(*parms)
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN3.py", line 2983, in db_read_image
return self.read_image_c(fsp, *parms, **kparms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xbd in position 2: invalid start byte
The MRCS files are written in 16bit float, so I thought this might be the problem.
If I run e2iminfo.py, I get the following:
e2iminfo.py -H FoilHole_31927214_Data_30931799_30931801_20231031_224012_fractions_shiny.mrcs | grep datatype
datatype: 0
datatype: 0
And If I try to convert a single polished stack.mrcs to .hdf using e2proc2d.py:
e2proc2d.py FoilHole_31927214_Data_30931799_30931801_20231031_224012_fractions_shiny.mrcs test.hdf
455 images, processing 0-454 stepping by 1
Traceback (most recent call last):
File "/home/mbelouso/anaconda3/envs/eman2/bin/e2proc2d.py", line 1173, in <module>
main()
File "/home/mbelouso/anaconda3/envs/eman2/bin/e2proc2d.py", line 608, in main
d.read_image(infile, i, False, None, False, img_type)
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN2.py", line 2956, in db_read_image
return self.read_image_c(fsp, *parms, **kparms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 0: invalid continuation byte
455 images, processing 0-454 stepping by 1
Traceback (most recent call last):
File "/home/mbelouso/anaconda3/envs/eman2/bin/e2proc2d.py", line 1173, in <module>
main()
File "/home/mbelouso/anaconda3/envs/eman2/bin/e2proc2d.py", line 608, in main
d.read_image(infile, i, False, None, False, img_type)
File "/home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/EMAN2.py", line 2956, in db_read_image
return self.read_image_c(fsp, *parms, **kparms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 0: invalid continuation byte
So I guess my question mostly is, does eman2 support the 16bit float as written out in RELION4 and RELION5? Or is there something I'm doing drastically wrong here?
thanks for your time,
cheers,
matt B
Ludtke, Steven J.
Nov 30, 2023, 9:20:34 PM11/30/23
to em...@googlegroups.com
No reason what you did shouldn't have worked. We've had several reported utf-8 decoding errors reported in the last week, all of them in different parts of the code, which seems to imply that there is some problem with the dependencies provided by Anaconda
right now. Looks like you built EMAN2 from source (which is good). Could you provide the output of
conda list
as well as the output of
ldd $CONDA_PREFIX/lib/python3.11/site-packages/libpyEMData2.so
We have not managed to reproduce this on any of our systems yet, which is making debugging very tricky...
---
Steven Ludtke, Ph.D. <slu...@bcm.edu> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry
Deputy Director, Advanced Technology Cores and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center
Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry
Deputy Director, Advanced Technology Cores and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center
--
--
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Matthew Belousoff
Nov 30, 2023, 9:26:10 PM11/30/23
to em...@googlegroups.com
Thanks for getting back so quickly! See the output below:
ldd $CONDA_PREFIX/lib/python3.11/site-packages/libpyEMData2.so
linux-vdso.so.1 (0x00007fff36be4000)
libEM2.so => /home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/libEM2.so (0x00007f5885e5f000)
libboost_python311.so.1.78.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libboost_python311.so.1.78.0 (0x00007f5885e22000)
libpython3.11.so.1.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libpython3.11.so.1.0 (0x00007f588585f000)
libstdc++.so.6 => /home/mbelouso/anaconda3/envs/eman2/lib/libstdc++.so.6 (0x00007f588567c000)
libgcc_s.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/libgcc_s.so.1 (0x00007f5885661000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5885420000)
libgsl.so.25 => /home/mbelouso/anaconda3/envs/eman2/lib/libgsl.so.25 (0x00007f5885119000)
libopenblas.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libopenblas.so.0 (0x00007f5882f50000)
libtiff.so.6 => /home/mbelouso/anaconda3/envs/eman2/lib/libtiff.so.6 (0x00007f5882ec2000)
libjpeg.so.8 => /home/mbelouso/anaconda3/envs/eman2/lib/libjpeg.so.8 (0x00007f5882e18000)
libpng16.so.16 => /home/mbelouso/anaconda3/envs/eman2/lib/libpng16.so.16 (0x00007f5882ddc000)
libhdf5.so.310 => /home/mbelouso/anaconda3/envs/eman2/lib/libhdf5.so.310 (0x00007f58829ae000)
libfftw3f.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3f.so.3 (0x00007f588277c000)
libfftw3.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3.so.3 (0x00007f5882555000)
libfftw3f_threads.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3f_threads.so.3 (0x00007f588254c000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5882465000)
libmvec.so.1 => /lib/x86_64-linux-gnu/libmvec.so.1 (0x00007f5882368000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f5882361000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f588235c000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f5882357000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5882352000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5886786000)
libgfortran.so.5 => /home/mbelouso/anaconda3/envs/eman2/lib/./libgfortran.so.5 (0x00007f58821a7000)
libwebp.so.7 => /home/mbelouso/anaconda3/envs/eman2/lib/./libwebp.so.7 (0x00007f5882105000)
libzstd.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./libzstd.so.1 (0x00007f5881ff1000)
liblzma.so.5 => /home/mbelouso/anaconda3/envs/eman2/lib/./liblzma.so.5 (0x00007f5881fc8000)
libLerc.so.4 => /home/mbelouso/anaconda3/envs/eman2/lib/./libLerc.so.4 (0x00007f5881f05000)
libdeflate.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/./libdeflate.so.0 (0x00007f5881ef0000)
libz.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./libz.so.1 (0x00007f5881ed5000)
libcrypto.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./libcrypto.so.3 (0x00007f58819c5000)
libcurl.so.4 => /home/mbelouso/anaconda3/envs/eman2/lib/./libcurl.so.4 (0x00007f588190b000)
libsz.so.2 => /home/mbelouso/anaconda3/envs/eman2/lib/./libsz.so.2 (0x00007f58818fe000)
libquadmath.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/././libquadmath.so.0 (0x00007f58818c5000)
libsharpyuv.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/././libsharpyuv.so.0 (0x00007f58818bb000)
libnghttp2.so.14 => /home/mbelouso/anaconda3/envs/eman2/lib/././libnghttp2.so.14 (0x00007f588188d000)
libssh2.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/././libssh2.so.1 (0x00007f5881848000)
libssl.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/././libssl.so.3 (0x00007f58817a6000)
libgssapi_krb5.so.2 => /home/mbelouso/anaconda3/envs/eman2/lib/././libgssapi_krb5.so.2 (0x00007f5881753000)
libkrb5.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkrb5.so.3 (0x00007f588167d000)
libk5crypto.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libk5crypto.so.3 (0x00007f5881663000)
libcom_err.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libcom_err.so.3 (0x00007f588165d000)
libkrb5support.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkrb5support.so.0 (0x00007f588164f000)
libkeyutils.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkeyutils.so.1 (0x00007f5881648000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f5881634000)
linux-vdso.so.1 (0x00007fff36be4000)
libEM2.so => /home/mbelouso/anaconda3/envs/eman2/lib/python3.11/site-packages/libEM2.so (0x00007f5885e5f000)
libboost_python311.so.1.78.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libboost_python311.so.1.78.0 (0x00007f5885e22000)
libpython3.11.so.1.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libpython3.11.so.1.0 (0x00007f588585f000)
libstdc++.so.6 => /home/mbelouso/anaconda3/envs/eman2/lib/libstdc++.so.6 (0x00007f588567c000)
libgcc_s.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/libgcc_s.so.1 (0x00007f5885661000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5885420000)
libgsl.so.25 => /home/mbelouso/anaconda3/envs/eman2/lib/libgsl.so.25 (0x00007f5885119000)
libopenblas.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/libopenblas.so.0 (0x00007f5882f50000)
libtiff.so.6 => /home/mbelouso/anaconda3/envs/eman2/lib/libtiff.so.6 (0x00007f5882ec2000)
libjpeg.so.8 => /home/mbelouso/anaconda3/envs/eman2/lib/libjpeg.so.8 (0x00007f5882e18000)
libpng16.so.16 => /home/mbelouso/anaconda3/envs/eman2/lib/libpng16.so.16 (0x00007f5882ddc000)
libhdf5.so.310 => /home/mbelouso/anaconda3/envs/eman2/lib/libhdf5.so.310 (0x00007f58829ae000)
libfftw3f.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3f.so.3 (0x00007f588277c000)
libfftw3.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3.so.3 (0x00007f5882555000)
libfftw3f_threads.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/libfftw3f_threads.so.3 (0x00007f588254c000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5882465000)
libmvec.so.1 => /lib/x86_64-linux-gnu/libmvec.so.1 (0x00007f5882368000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f5882361000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f588235c000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f5882357000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5882352000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5886786000)
libgfortran.so.5 => /home/mbelouso/anaconda3/envs/eman2/lib/./libgfortran.so.5 (0x00007f58821a7000)
libwebp.so.7 => /home/mbelouso/anaconda3/envs/eman2/lib/./libwebp.so.7 (0x00007f5882105000)
libzstd.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./libzstd.so.1 (0x00007f5881ff1000)
liblzma.so.5 => /home/mbelouso/anaconda3/envs/eman2/lib/./liblzma.so.5 (0x00007f5881fc8000)
libLerc.so.4 => /home/mbelouso/anaconda3/envs/eman2/lib/./libLerc.so.4 (0x00007f5881f05000)
libdeflate.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/./libdeflate.so.0 (0x00007f5881ef0000)
libz.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./libz.so.1 (0x00007f5881ed5000)
libcrypto.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./libcrypto.so.3 (0x00007f58819c5000)
libcurl.so.4 => /home/mbelouso/anaconda3/envs/eman2/lib/./libcurl.so.4 (0x00007f588190b000)
libsz.so.2 => /home/mbelouso/anaconda3/envs/eman2/lib/./libsz.so.2 (0x00007f58818fe000)
libquadmath.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/././libquadmath.so.0 (0x00007f58818c5000)
libsharpyuv.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/././libsharpyuv.so.0 (0x00007f58818bb000)
libnghttp2.so.14 => /home/mbelouso/anaconda3/envs/eman2/lib/././libnghttp2.so.14 (0x00007f588188d000)
libssh2.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/././libssh2.so.1 (0x00007f5881848000)
libssl.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/././libssl.so.3 (0x00007f58817a6000)
libgssapi_krb5.so.2 => /home/mbelouso/anaconda3/envs/eman2/lib/././libgssapi_krb5.so.2 (0x00007f5881753000)
libkrb5.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkrb5.so.3 (0x00007f588167d000)
libk5crypto.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libk5crypto.so.3 (0x00007f5881663000)
libcom_err.so.3 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libcom_err.so.3 (0x00007f588165d000)
libkrb5support.so.0 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkrb5support.so.0 (0x00007f588164f000)
libkeyutils.so.1 => /home/mbelouso/anaconda3/envs/eman2/lib/./././libkeyutils.so.1 (0x00007f5881648000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f5881634000)
conda list
# packages in environment at /home/mbelouso/anaconda3/envs/eman2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.0.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.9.1 py311h459d7ec_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
anyio 4.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.13.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
biopython 1.81 py311h459d7ec_1 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
boost 1.78.0 py311h92ebd52_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py311hb755f60_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.23.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.2 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311hb3a22ac_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cmake 3.27.9 hcfe8598_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
configparser 5.3.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py311h9547e67_0 conda-forge
cryptography 41.0.5 py311h63ff55d_0 conda-forge
cuda-version 11.8 h70ddcb2_2 conda-forge
cudatoolkit 11.8.0 h4ba93d1_12 conda-forge
cudnn 8.8.0.121 hcdd5f01_4 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.0 py311hb755f60_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 mpi_openmpi_h4a81ba8_8 conda-forge
flatbuffers 23.5.26 h59595ed_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.45.1 py311h459d7ec_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
frozenlist 1.4.0 py311h459d7ec_1 conda-forge
ftgl 2.4.0 h6cc6478_2 cryoem
future 0.18.3 pyhd8ed1ab_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
glib 2.78.1 hfc55251_1 conda-forge
glib-tools 2.78.1 hfc55251_1 conda-forge
google-auth 2.24.0 pyhca7485f_0 conda-forge
google-auth-oauthlib 1.0.0 pyhd8ed1ab_1 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
grpcio 1.54.3 py311hcafe171_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.22.7 h8e1006c_0 conda-forge
gstreamer 1.22.7 h98fc4e7_0 conda-forge
h5py 3.10.0 nompi_py311h3839ddf_100 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf5 1.14.2 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.26.0 pyhf8b6a83_0 conda-forge
ipython 8.18.1 pyh31011fe_1 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jax 0.4.19 pyhd8ed1ab_0 conda-forge
jaxlib 0.4.14 cuda112py311hf2474b9_201 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h38be061_3 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.20.0 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.0 py311h38be061_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.11.1 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.9 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
keras 2.12.0 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py311h9547e67_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230125.3 cxx17_h59595ed_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libclang 15.0.7 default_h7634d5b_3 conda-forge
libclang13 15.0.7 default_h9986a30_3 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libglib 2.78.1 h783c2da_1 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libgrpc 1.54.3 hb20ce57_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 hd590300_1 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libllvm15 15.0.7 h5cf9203_3 conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 15.4 hfc447b1_2 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libsystemd0 254 h3516f8a_0 conda-forge
libtiff 4.5.1 h8b53f26_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.46.0 hd590300_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxkbcommon 1.6.0 h5d7e998_0 conda-forge
libxml2 2.11.6 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markdown 3.5.1 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py311h459d7ec_1 conda-forge
matplotlib 3.8.2 py311h38be061_0 conda-forge
matplotlib-base 3.8.2 py311h54ef318_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
ml_dtypes 0.3.1 py311h320fe9a_2 conda-forge
mpg123 1.32.3 h59595ed_0 conda-forge
mpi 1.0 openmpi conda-forge
multidict 6.0.4 py311h459d7ec_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.11.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
nccl 2.19.4.1 h6103f9b_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge
nodejs 20.9.0 hb753e55_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.95 h1d7d5a4_0 conda-forge
numpy 1.23.5 py311h7d28db0_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.1.4 hd590300_0 conda-forge
opt-einsum 3.3.0 hd8ed1ab_2 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.1.3 py311h320fe9a_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.0 py311h0b84326_0 conda-forge
pip 23.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.42.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
prometheus_client 0.19.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.41 pyha770c72_0 conda-forge
protobuf 4.21.12 py311hcafe171_0 conda-forge
psutil 5.9.5 py311h459d7ec_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydusa 3.1 np123py311h5c49d3a_7 cryoem
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.5 py_0 cryoem
pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py311hf0fb5b6_5 conda-forge
pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.11.6 hab00c5b_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge
python-flatbuffers 23.5.26 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311h459d7ec_1 conda-forge
pyzmq 25.1.1 py311h34ded2d_2 conda-forge
qt-main 5.15.8 hc47bfe8_16 conda-forge
re2 2023.03.02 h8c504da_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.31.1 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rhash 1.4.4 hd590300_0 conda-forge
rpds-py 0.13.2 py311h46250e7_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
scikit-learn 1.3.2 py311hc009520_1 conda-forge
scipy 1.11.4 py311h64a7726_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py311hb755f60_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sphire 1.4.3 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
tensorboard 2.12.3 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py311h63ff55d_1 conda-forge
tensorflow 2.12.1 cuda112py311h63ba870_1 conda-forge
tensorflow-base 2.12.1 cuda112py311hb4f7669_1 conda-forge
tensorflow-estimator 2.12.1 cuda112py311h9aaad64_1 conda-forge
termcolor 2.3.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.0 pyh0d859eb_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py311h459d7ec_1 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.14.0 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge
typing-extensions 4.5.0 hd8ed1ab_0 conda-forge
typing_extensions 4.5.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge
werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py311h459d7ec_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.40 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.3 py311h459d7ec_0 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
# packages in environment at /home/mbelouso/anaconda3/envs/eman2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.0.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.9.1 py311h459d7ec_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
anyio 4.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.13.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
biopython 1.81 py311h459d7ec_1 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
boost 1.78.0 py311h92ebd52_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py311hb755f60_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.23.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.2 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311hb3a22ac_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cmake 3.27.9 hcfe8598_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
configparser 5.3.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py311h9547e67_0 conda-forge
cryptography 41.0.5 py311h63ff55d_0 conda-forge
cuda-version 11.8 h70ddcb2_2 conda-forge
cudatoolkit 11.8.0 h4ba93d1_12 conda-forge
cudnn 8.8.0.121 hcdd5f01_4 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.0 py311hb755f60_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 mpi_openmpi_h4a81ba8_8 conda-forge
flatbuffers 23.5.26 h59595ed_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.45.1 py311h459d7ec_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
frozenlist 1.4.0 py311h459d7ec_1 conda-forge
ftgl 2.4.0 h6cc6478_2 cryoem
future 0.18.3 pyhd8ed1ab_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
glib 2.78.1 hfc55251_1 conda-forge
glib-tools 2.78.1 hfc55251_1 conda-forge
google-auth 2.24.0 pyhca7485f_0 conda-forge
google-auth-oauthlib 1.0.0 pyhd8ed1ab_1 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
grpcio 1.54.3 py311hcafe171_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.22.7 h8e1006c_0 conda-forge
gstreamer 1.22.7 h98fc4e7_0 conda-forge
h5py 3.10.0 nompi_py311h3839ddf_100 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf5 1.14.2 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.26.0 pyhf8b6a83_0 conda-forge
ipython 8.18.1 pyh31011fe_1 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jax 0.4.19 pyhd8ed1ab_0 conda-forge
jaxlib 0.4.14 cuda112py311hf2474b9_201 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h38be061_3 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.20.0 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.0 py311h38be061_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.11.1 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.9 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
keras 2.12.0 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py311h9547e67_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230125.3 cxx17_h59595ed_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libclang 15.0.7 default_h7634d5b_3 conda-forge
libclang13 15.0.7 default_h9986a30_3 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libglib 2.78.1 h783c2da_1 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libgrpc 1.54.3 hb20ce57_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 hd590300_1 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libllvm15 15.0.7 h5cf9203_3 conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 15.4 hfc447b1_2 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libsystemd0 254 h3516f8a_0 conda-forge
libtiff 4.5.1 h8b53f26_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.46.0 hd590300_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxkbcommon 1.6.0 h5d7e998_0 conda-forge
libxml2 2.11.6 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markdown 3.5.1 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 py311h459d7ec_1 conda-forge
matplotlib 3.8.2 py311h38be061_0 conda-forge
matplotlib-base 3.8.2 py311h54ef318_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
ml_dtypes 0.3.1 py311h320fe9a_2 conda-forge
mpg123 1.32.3 h59595ed_0 conda-forge
mpi 1.0 openmpi conda-forge
multidict 6.0.4 py311h459d7ec_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.11.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
nccl 2.19.4.1 h6103f9b_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge
nodejs 20.9.0 hb753e55_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.95 h1d7d5a4_0 conda-forge
numpy 1.23.5 py311h7d28db0_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.1.4 hd590300_0 conda-forge
opt-einsum 3.3.0 hd8ed1ab_2 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.1.3 py311h320fe9a_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.0 py311h0b84326_0 conda-forge
pip 23.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.42.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
prometheus_client 0.19.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.41 pyha770c72_0 conda-forge
protobuf 4.21.12 py311hcafe171_0 conda-forge
psutil 5.9.5 py311h459d7ec_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydusa 3.1 np123py311h5c49d3a_7 cryoem
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.5 py_0 cryoem
pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py311hf0fb5b6_5 conda-forge
pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.11.6 hab00c5b_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge
python-flatbuffers 23.5.26 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311h459d7ec_1 conda-forge
pyzmq 25.1.1 py311h34ded2d_2 conda-forge
qt-main 5.15.8 hc47bfe8_16 conda-forge
re2 2023.03.02 h8c504da_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.31.1 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rhash 1.4.4 hd590300_0 conda-forge
rpds-py 0.13.2 py311h46250e7_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
scikit-learn 1.3.2 py311hc009520_1 conda-forge
scipy 1.11.4 py311h64a7726_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py311hb755f60_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sphire 1.4.3 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
tensorboard 2.12.3 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py311h63ff55d_1 conda-forge
tensorflow 2.12.1 cuda112py311h63ba870_1 conda-forge
tensorflow-base 2.12.1 cuda112py311hb4f7669_1 conda-forge
tensorflow-estimator 2.12.1 cuda112py311h9aaad64_1 conda-forge
termcolor 2.3.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.0 pyh0d859eb_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py311h459d7ec_1 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.14.0 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge
typing-extensions 4.5.0 hd8ed1ab_0 conda-forge
typing_extensions 4.5.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge
werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py311h459d7ec_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.40 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.3 py311h459d7ec_0 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
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Dr. Matthew Belousoff
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences &
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences &
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052
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Melbourne 3800
shadow walker
Nov 30, 2023, 10:16:09 PM11/30/23
to em...@googlegroups.com
Can you write the list of packages to a file, so it will be easier to recreate your environment?
conda list --explicit > environment.txt
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2B7zjsngYS3ZZBay6Yum2h0um6XY24iBA2S2f3aEpqO6vm7d1A%40mail.gmail.com.
Matthew Belousoff
Nov 30, 2023, 10:30:15 PM11/30/23
to em...@googlegroups.com
Its attached mate.
Thanks!
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shadow walker
Dec 3, 2023, 1:53:40 PM12/3/23
to em...@googlegroups.com
Thanks for the environment file. If you don't mind, can you also provide a minimal star file and the corresponding command that fails? Or, a file that fails with e2proc2d like in your original post along with the command? If you have updated your environment recently, the output of 'conda list -r' when your environment causing problems is activated. And, finally, for now, what OS distro are you on?
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--
shadow_walker
Matthew Belousoff
Dec 5, 2023, 5:26:40 PM12/5/23
to EMAN2
Hey mate,
Sorry for the delay. The files are attached and the distro is linux mint 21.2, kernel 5.15.0-89-generic. I may have to transfer the particle stack another way? Its 21M and a too big to share here. Happy to send it some other way though.
Thanks so much,
matt B
Steve Ludtke
Dec 7, 2023, 10:43:43 AM12/7/23
to em...@googlegroups.com
Ok, we have figured out what’s going on, at least why unicode errors are getting produced. When an exception is generated in C++ code, that exception is supposed to be passed to python and displayed as an error message. Sometime over the last few years, this mechanism in Boost Python (the library we use for Python <-> C++) seems to have broken, and it started printing random gibberish on the screen instead of a proper error message. It appears that sometime in Python 3.10 or 3.11, they further changed the mechanism so the string coming in from C++ was interpreted as Unicode instead of ASCII. So it’s still getting gibberish, but now it’s trying to treat it as unicode, producing another error.
SO, what that means, if you didn’t follow the above, is that any time you see one of these Unicode errors, that means that some exception/error occurred in the C++ code. If it prints a Python traceback, the point at which the exception occurred should be correct, but instead of printing a proper error message, it produces this unicode error instead. So rather than focus on the Unicode issue, the correct response is to look for what caused the underlying error.
Float16 is not a formal part of the MRC file specification (PMC4642651), so whomever decided to do this has yet again mucked up an already abused file format. While FLOAT16s can be extremely computationally efficient on GPUs, they have insufficient precision for anything other than storage of raw image data, which could be stored MUCH more efficiently in other ways (PMC9645247).
Anyway, if you can point at wherever FLOAT16 first emerged in publication (I missed it whereever it is), we should be able to add support for it pretty trivially.
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