Pb install latest version of eman2

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Marc Ruff

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Jul 29, 2025, 12:49:27 PMJul 29
to EMAN2
Hi all,
I tried to install the latest version of eman2.
I got the error on the cmake step:

[ 92%] Building CXX object rt/imageio/CMakeFiles/test_eer.dir/test_eer.cpp.o
[ 93%] Linking CXX executable test_eer
//usr/local/miniconda3/envs/eman2/lib/libLerc.so.4: undefined reference to `std::__throw_bad_array_new_length()@GLIBCXX_3.4.29'
collect2: error: ld returned 1 exit status
make[2]: *** [rt/imageio/CMakeFiles/test_eer.dir/build.make:109: rt/imageio/test_eer] Error 1
make[1]: *** [CMakeFiles/Makefile2:1233: rt/imageio/CMakeFiles/test_eer.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 94%] Building CXX object libpyEM/CMakeFiles/pyTypeConverter2.dir/typeconverter.cpp.o
[ 95%] Linking CXX shared library libpyGeometry2.so
[ 95%] Built target pyGeometry2
[ 96%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/emdata_wrapitems.cpp.o
[ 96%] Linking CXX shared library libpyBoxingTools2.so
[ 96%] Built target pyBoxingTools2
[ 97%] Linking CXX shared library libpyPointArray2.so
[ 97%] Built target pyPointArray2
[ 98%] Linking CXX shared library libpyTypeConverter2.so
[ 98%] Built target pyTypeConverter2
[ 98%] Linking CXX shared library libpyTransform2.so
[ 98%] Built target pyTransform2
[ 99%] Linking CXX shared library libpyUtils2.so
[ 99%] Built target pyUtils2
[100%] Linking CXX shared library libpyEMData2.so
[100%] Built target pyEMData2
make: *** [Makefile:146: all] Error 2

I join the problem report.

Thank you for your help,
Best,
Marc
PbInstallEman2.txt

Steve Ludtke

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Jul 29, 2025, 2:56:39 PMJul 29
to em...@googlegroups.com
Hi Marc,
at first glance this looks like C++ library version incompatibility with the packages you're getting from conda-forge. Can you double check that with the eman2 environment activated that you don't have LD_LIBRARY_PATH set in your shell? That's the first possibility that comes to mind.

If that isn't it, which linux distro and version are you running on the machine?  Do you have a reasonably up to date C compiler? (g++ --version)

It's also striking, however, that you only seem to be getting an error from a single program, which isn't actually used anywhere in EMAN2 (it was written by a programmer as he was developing the EER file reader). If you activate the eman2 environment and run "e2version.py" and "e2speedtest.py" do they run?  I may need to take a look at deactivating that pointless program. It's possible that the author did some stuff which requires a more up-to-date C++ library than anything else in the system. 

It looks like you're running the unit-tests. This isn't something we normally suggest end-users do, as there are frequently meaningless failures which we rarely bother with. They are really for (infrequent) use by the developers.

 
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Marc RUFF

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Jul 31, 2025, 11:42:37 PMJul 31
to em...@googlegroups.com

Hi  Steve,

Thank you for your prompt answer.

 

To answer your questions:

echo $LD_LIBRARY_PATH

nothing is set

 

which linux distro and version are you running on the machine:

Rocky Linux 8.7

 

G++ --version

g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-15)

 

If you activate the eman2 environment and run "e2version.py" and "e2speedtest.py" do they run?  

No

 

In addition, the output of cmake shows these errors:

.

.

.

-- Configuring done (1.5s)

CMake Warning at libpyEM/CMakeLists.txt:2 (add_library):

  Cannot generate a safe runtime search path for target pyGLUtils2 because

  files in some directories may conflict with libraries in implicit

  directories:

 

    runtime library [libGLX.so.0] in /usr/lib64 may be hidden by files in:

      /usr/local/miniconda3/envs/eman2/lib

    runtime library [libOpenGL.so.0] in /usr/lib64 may be hidden by files in:

      /usr/local/miniconda3/envs/eman2/lib

 

  Some of these libraries may not be found correctly.

Call Stack (most recent call first):

  libpyEM/CMakeLists.txt:46 (ADD_PYSTE_LIB)

 

 

CMake Warning at libpyEM/CMakeLists.txt:2 (add_library):

  Cannot generate a safe runtime search path for target pyMarchingCubes2

  because files in some directories may conflict with libraries in implicit

  directories:

 

    runtime library [libGLX.so.0] in /usr/lib64 may be hidden by files in:

      /usr/local/miniconda3/envs/eman2/lib

    runtime library [libOpenGL.so.0] in /usr/lib64 may be hidden by files in:

      /usr/local/miniconda3/envs/eman2/lib

 

  Some of these libraries may not be found correctly.

Call Stack (most recent call first):

  libpyEM/CMakeLists.txt:47 (ADD_PYSTE_LIB)

 

 

-- Generating done (0.1s)

.

.

 

Thank you !

Best,

Marc

 

 

De : em...@googlegroups.com <em...@googlegroups.com> De la part de Steve Ludtke
Envoyé : mardi 29 juillet 2025 20:56
À : em...@googlegroups.com
Objet : Re: [EMAN2] Pb install latest version of eman2

Steve Ludtke

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Aug 1, 2025, 12:05:23 AMAug 1
to em...@googlegroups.com
Hi Marc,
See below

On Jul 30, 2025, at 4:26 AM, 'Marc RUFF' via EMAN2 <em...@googlegroups.com> wrote:

Hi  Steve,
Thank you for your prompt answer.
 
To answer your questions:
echo $LD_LIBRARY_PATH
nothing is set
Ok, that's good.

 
which linux distro and version are you running on the machine:
Rocky Linux 8.7
 
G++ --version
g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-15)
The default compiler on Rocky, like RedHat, is part of a pretty old series. It appears that Rocky 8.7 does support newer compiler chain (GCC 12 toolset)  which _might_ make a difference. 
Those are actually just warnings. While they do indicate some inconsistencies in your setup, they shouldn't actually cause a problem.

 
-- Generating done (0.1s)

Ok, I'm still not positive what's causing your failure. It could still be an issue with a mixing of C++ versions, which could be solved by installing and using a GCC12 toolchain. 

However, there is an easier test you can run. Since the only failure you seem to be having is with a useless test. When you run cmake, try adding "-DENABLE_RT=OFF" then try compiling again.

Steve Ludtke

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Aug 4, 2025, 8:42:22 AMAug 4
to Steve Ludtke, em...@googlegroups.com
Hi, given some of the recent problems people seem to have installing. I tried a binary installation (not source compile) from scratch on a Rocky 8.7 fresh install, and it worked without any issues. Two steps:

- Install MiniForge: https://github.com/conda-forge/miniforge/releases (reopen shell after)
- conda create -n eman2 eman-dev -c cryoem -c conda-forge

Marc RUFF

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Aug 4, 2025, 8:46:50 PMAug 4
to em...@googlegroups.com

Hi Steve,

Adding "-DENABLE_RT=OFF" worked !

All looks fine now.

Thank you very much for your help.

Best,

Marc

 

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Marc Ruff

IGBMC, 1 rue Laurent Fries

67404, Illkirch, France

E-mail : ru...@igbmc.fr

Tel : +33 3 69 48 52 95

Mob : +33 6 03 09 59 61

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De : em...@googlegroups.com <em...@googlegroups.com> De la part de Steve Ludtke
Envoyé : vendredi 1 août 2025 06:05

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