e2speedtest.py Error

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Henry Wietfeldt

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Jul 15, 2022, 2:51:42 PM7/15/22
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Hi,

I recently installed the binary for eman2.91 on MacOS Catalina, following the instructions at https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.91. When I run e2speedtest.py, I get the following error:

(base) [xxx]:~ wietfeldthc$ e2speedtest.py
Traceback (most recent call last):
  File "/Users/wietfeldthc/eman2-sphire-sparx/bin/e2speedtest.py", line 43, in <module>
    from EMAN2 import *
  File "/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2.py", line 49, in <module>
    from EMAN2_cppwrap import *
  File "/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_cppwrap.py", line 33, in <module>
    from libpyAligner2 import *
ImportError: dlopen(/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/libpyAligner2.so, 2): Library not loaded: @rpath/libboost_python37.dylib
  Referenced from: /Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/libpyAligner2.so
  Reason: image not found
(base) [xxx]:~ wietfeldthc$

The environment variables PYTHONPATH, PYTHONHOME, LD_LIBRARY_PATH or DYLD_LIBRARY_PATH are not set.  My active conda environment is the eman2 directory.  After first installing the binary, when I ran e2speedtest.py, I got the ModuleNotFoundError: No module named 'past' error described in the Troubleshooting guide.  Then I manually installed the dependencies using conda install eman-deps=25 -c cryoem -c defaults -c conda-forge as suggested.  Afterwards, when I ran e2speedtest.py, I got the same ModuleNotFoundError: No module named 'past' error, so I ran the command conda install future.  Then when I ran e2speedtest.py, I got the error ModuleNotFoundError: No module named 'numpy', so I ran the command conda install numpy.  Now when I run e2speedtest.py, I get the error message pasted above.  I get this same error message for all the test commands, except for e2version.py, which runs successfully.  When I run e2version.py, I get the following output:

(base) [xxx]:~ wietfeldthc$ e2version.py
EMAN 2.91 final ( GITHUB: 2021-03-08 12:05 - commit: 81caed2 )
Your EMAN2 is running on: Mac OS 10.15.7 x86_64
Your Python version is: 3.7.10
(base) [xxx]:~ wietfeldthc$

I believe that I'm getting this issue because I'm not installing the dependencies correctly.  What do you suggest I do?  Thank you!

Henry

Henry Wietfeldt

Postbaccalaureate CRTA Fellow

Elmlund Lab| Cryo-EM

National Cancer Institute

Henry Wietfeldt

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Jul 19, 2022, 4:19:06 PM7/19/22
to EMAN2
I solved this error by adding the following to my .condarc file:

channel_priority: strict 
channels: 
     - conda-forge 
     - defaults

If anyone encounters a similar issue, these pages are good guides:
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