Category Archives: EM

CCP-EM install on CentOS 7

The CCP-EM software suite is a package containing tools for cryo-EM. You can find it here. I want to install it together with the already existing software. The Brief instructions seem to work fine, provided you have the requirements. This … Continue reading

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crYOLO conda error: bad interpreter

Creating a new virtual environment for crYOLO, that implement You Only Look Once for particle picking, I stumbled upon this error. I saw it before, but here we don’t use python so much, I mean, we use it only for … Continue reading

Posted in bits, centos, EM, linux, modules, python, software, sphire | Leave a comment

A leginon docker on CentOS 7 Part II: centos7AutoInstallation.py

On the previous post, we prepared a basic LAMP docker to hold a leginon installation.¬† I assume now you downloaded the installer for CentOS 7 and copied it to the docker via ssh or shared folder. We can simply run … Continue reading

Posted in bits, centos, containers, docker, EM, filesystems, leginon, linux, modules, mysql, yum | 1 Comment

A leginon docker on CentOS 7 Part I: docker and database server install

Previously we we made a leginon CentOS 6 container on CentOS 7. Now the LXC containers are somehow more robust than a docker, but less popular and versatile. Therefore the need to make a docker instead. I start by cloning … Continue reading

Posted in bash, centos, containers, docker, EM, leginon, linux, python, yum | 2 Comments

ImportError: /lib64/libc.so.6: version `GLIBC_2.18′ not found on CentOS 7

I don’t have a solution for this one, but I managed to go ahead with different settings. I got this package from a colleague that is supposed to be of general interest. It does come with a binary inside, and … Continue reading

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/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20′ not found CentOS 7

The GLIBCXX error is a recurrent one. It happens usually when I try to use new code¬†just compiled on an old system. The old system is my CentOS 7. I got it prevously, for example installing relion 2.1. But I … Continue reading

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A relion 2.1.stable module for CentOS 7

There is a new relion to add to the collection. You can find the installation details here. I will tell you my experience doing as suggested. First thing that it calls my attention on the github instructions is that they … Continue reading

Posted in bits, centos, EM, GPU, hardware, linux, modules, python | 1 Comment