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I am trying to install pymol in CentOS 7 system. I installed the dependency glm-devel-0.9.6.3-1.el7.noarch by yum:

sudo yum install glm-devel.

During compiling I got an error related to glm as following:

layer1/SceneView.cpp:34:61: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’

Could anyone tell why this error appears? I will appreciate any help!

Best regards.

Sadra M.
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Yeping Sun
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1 Answers1

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install pymol in CentOS 7

Build example with updated glm-devel

# yum install mmtf-cpp-devel.x86_64 glew-devel.x86_64 libpng-devel freetype-devel msgpack-devel libxml2-devel python36-qt5-devel.x86_64  freeglut-devel mesa-libGL-devel.x86_64 python3-devel

# yum install ./glm-devel-0.9.9.6-6.el7.noarch.rpm
     ## works with the default python3 (3.6.8) and g++ -4.8.5

Link, glm-devel-0.9.9.6-6.el7 https://drive.google.com/file/d/1BXygEWqpvlbZg867dsXuW47T67Z0V0Q8/view?usp=sharing

https://github.com/schrodinger/pymol-open-source → https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL

git clone https://github.com/schrodinger/pymol-open-source.git
cd pymol-open-source/
python3 setup.py build

# python3 setup.py install

pymol       ## the pymol GUI opens OK

There is also a binary version available, with python 3.7 included : https://pymol.org/2/ → https://pymol.org/installers/PyMOL-2.5.2_293-Linux-x86_64-py37.tar.bz2 → tar xvf PyMOL-2.5.2_293-Linux-x86_64-py37.tar.bz2

cd pymol/ && ./pymol

Knud Larsen
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  • I reinstalled glm-devel downloaded from the link you gave, and installed python from source. I got a now error related to glm: "layer1/SceneView.cpp:8:49: fatal error: glm/detail/func_vector_relational.hpp: No such file or directory". Looks like there is still something wrong with glm – Yeping Sun Sep 12 '21 at 16:22
  • I've copied the detail/func_vector_relational.hpp from the older version. Now many new errors come up. The first one says: {/usr/include/glm/detail/precision.hpp:37:7: error: using typedef-name ‘glm::precision’ after ‘enum’ }. How to fix it? – Yeping Sun Sep 12 '21 at 17:21
  • The python version is 3.6.8. The glm version is 0.9.8.5-2.el7. The errors include: (1) "contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:27:20: fatal error: netcdf.h: No such file or directory"; (2) "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory"; (3) layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)" – Yeping Sun Sep 13 '21 at 10:50
  • Please read the edited answer, which emphasizes what's working : pymol from github + The "default python3 (3.6.8) and the default g++ -4.8.5" + glm-devel-**0.9.9.6**-6.el7 – Knud Larsen Sep 13 '21 at 12:14