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cluster:215 [2025/09/24 17:22] – [Miniconda3-py313] hmeij07cluster:215 [2025/12/10 15:07] (current) – [Structure] hmeij07
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   * module load miniconda3/py313   * module load miniconda3/py313
     * loads conda modules and ncbi-blast     * loads conda modules and ncbi-blast
 +  * (cummingsgroup)
  
 **QIIME** **QIIME**
Line 66: Line 67:
 (base)  (base) 
  
-# 5 python modules installed+# 1-5 python modules installed
  
 # ncbi-blast downloaded from https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/   # ncbi-blast downloaded from https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/  
 export PATH=/share/apps/CENTOS8/ohpc/software/ncbi-blast/2.17.0+/bin:$PATH export PATH=/share/apps/CENTOS8/ohpc/software/ncbi-blast/2.17.0+/bin:$PATH
  
-# all 4 other packages installed via pip or conda minus vsearch+# all 6-10 other packages installed via pip or conda 
 # brew install vsearch is a mac command, x86_64 binary not glibc compatible # brew install vsearch is a mac command, x86_64 binary not glibc compatible
 # success with conda install vsearch # success with conda install vsearch
Line 161: Line 162:
  
 </code> </code>
 +
 +===== Quantum Espresso =====
 +
 +  * module q-e/7.3
 +  * Description:  Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. 
 +  * URL https://www.quantum-espresso.org/ 
 +  * /share/apps/CENTOS8/ohpc/software/q-e/7.3/bin
 +  * openmp and openmpi enabled, no cuda
  
 ===== Structure ===== ===== Structure =====
Line 440: Line 449:
 </code> </code>
  
-  * **g_mmpba**+  * **g_mmpba and gmx_MMPBSA**
   * https://g-mmpbsa.readthedocs.io/en/latest/install.html   * https://g-mmpbsa.readthedocs.io/en/latest/install.html
   * calterlab (Kayla)   * calterlab (Kayla)
Line 453: Line 462:
 Installing collected packages: g_mmpbsa Installing collected packages: g_mmpbsa
 Successfully installed g_mmpbsa-3.0.9 Successfully installed g_mmpbsa-3.0.9
 +
 +# works?
 +
 +ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
 +pygmtsar 2024.8.30.post3 requires pandas>=2.2, but you have pandas 1.5.3 which is incompatible.
 +dask-expr 1.1.14 requires pandas>=2, but you have pandas 1.5.3 which is incompatible.
 +xarray 2024.9.0 requires pandas>=2.1, but you have pandas 1.5.3 which is incompatible.
 +
 +Successfully installed gmx_MMPBSA-1.6.4 matplotlib-3.7.3 mpi4py-4.0.1 numpy-1.26.4 pandas-1.5.3 parmed-4.3.0 scipy-1.14.1 seaborn-0.11.2
 +
 +gmx-mmpbsa 1.6.4 requires pandas==1.5.3, but you have pandas 2.2.0 which is incompatible.
 +Successfully installed pandas-2.2.0
 +
 +# back to
 +Successfully installed pandas-1.5.3
  
  
cluster/215.1758734569.txt.gz · Last modified: by hmeij07