Installation - HackMD

Matlab engine Ref: https://pypi.org/project/matlabengine/ https://www.mathworks.com/help/matlab/matlab_external/install-the-matlab-engine-for-python.html ```conda create -n matlab python=3.7 conda activate matlab cd <matlabroot>/extern/engines/python mkdir build sudo chmod 777 build python setup.py install ``` # Conda ## Miniconda - Download link: [miniconda linux](https://www.anaconda.com/docs/getting-started/miniconda/install#macos-linux-installation:to-download-a-different-version) ```bash= DIR=$HOME/miniconda3 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh -b -p $DIR source $DIR/bin/activate conda init # Install ... conda create --name <your_env_name> python=<python_version> # e.g., your_env_name=test, python_version=3.11 pip install -r requirements.txt ``` ## Anaconda Installation website: https://www.anaconda.com/download#downloads Choose proper version for Operating System, get the link ```bash= # Download the installation file (e.g. Linux 64-Bit (x86) Installer (860 MB)) wget https://repo.anaconda.com/archive/Anaconda3-2023.03-1-Linux-x86_64.sh # Run the Anaconda installation script with the following command: bash Anaconda3-2023.03-1-Linux-x86_64.sh # Activate the Anaconda environment source ~/anaconda3/bin/activate # Create new environments conda create --name myenv # Activate the new environment conda activate myenv # wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh # bash Miniconda3-latest-Linux-x86_64.sh # conda create -n myenv python=3.7 # conda activate myenv ``` ## Conda environment transferation across devices ```bash= # Check conda env (base) loci@Mac:~$ conda env list # Head to loci_env (loci_env) loci@Mac:~$ conda activate loci_env # Export loci_env (loci_env) loci@Mac:~$ conda env export > loci_env.yml # Location loci_env.yml file to another device # Create new env from loci_env.yml file (base) loci@Typhoon:~$ conda env create -f loci.yml # Activate loci_env (loci_env) loci@Typhoon:~$ conda activate loci_env ``` # MATLAB To get MATLAB lisence through NTHU, one needs to register NTHU email account (e.g. s111080421@m111.nthu.edu.tw) from [ccxp](https://www.ccxp.nthu.edu.tw/ccxp/INQUIRE/index.php?lang=english) system. Check this [instruction](https://learning.site.nthu.edu.tw/var/file/319/1319/img/2902/1090423NationalTsingHuaUniversity_ENGInstallationGuideline-V9.pdf). 1. Log in using NTHU account ![](https://hackmd.io/_uploads/rJY4nc1fa.png) 2. Download installation file Download: https://www.mathworks.com/downloads/ E.g.: matlab_R2023a_glnxa64.zip 3. Install MATLAB on [Ubuntu](https://www.mathworks.com/matlabcentral/answers/518584-how-do-i-install-on-ubuntu) ```bash= cd /opt/matlab_R2023a_glnxa64 chmod +x ./* cd /opt/matlab_R2023a_glnxa64/bin/glnxa64 chmod +x ./* cd /opt/matlab_R2023a_glnxa64 ./install ``` Up to now, if the Matlab Installer does not start, use the command below to fix the error. ```bash= xhost +SI:localuser:root ``` ## Docker MATLAB images: https://hub.docker.com/r/mathworks/matlab Docker engine version: https://www.mathworks.com/support/requirements/python-compatibility.html 4. [Manually Activate Software on a Computer](https://www.mathworks.com/licensecenter/licenses/40638624/4628136/activations) Step 1: Access to *License Center* Step 2: Tag *Install and Activate* Step 3: *View activated computers* Step 4: *Activated a computer* Step 5: Fill the form The form should be filled out as follows (A100 machine): ``` Release: R2023a. Operating System: Linux Host ID: Enter the MAC address of your primary network interface without colons. If eth0 is your primary network interface, the Host ID would be ==00163eaa5605==. Computer Login Name: yang_loci (as indicated by your command prompt) Activation Label: yang_loci (or any other label you prefer) ``` ![Screenshot 2024-11-28 at 5.16.15 PM](https://hackmd.io/_uploads/SkRJHhS7ke.png) Note: ``` # Host ID (MAC Address of Primary Network Interface): ip link show ifconfig -a | grep ether # Find the Host ID in the License File grep -i "hostid" license.lic ``` # Others ## CHARMM Installation pyCHARM http://charmm.chemistry.harvard.edu/main.php Instruction pyCHARM https://academiccharmm.org/documentation/installation#Install ## Modeller Anaconda: https://anaconda.org/salilab/modeller Modeller instr: https://salilab.org/modeller/10.4/release.html#osx Registration for non-academic license: https://salilab.org/modeller/registration.html Modify license key in /Users/loctran/opt/anaconda3/envs/modeller_env/lib/modeller-10.4/modlib/modeller/config.py file ```python install_dir = r'/Users/loctran/opt/anaconda3/envs/modeller_env/lib/modeller-10.4' license = r'MODELIRANJE' ``` Run conda install `conda install -c salilab modeller` ## CMake > Download: https://cmake.org/download/ > Installing CMake: https://cmake.org/install/ ```bash # apt or sudo apt apt update apt install gcc export CC=gcc apt install g++ export CXX=g++ apt install make export MAKE=make apt-get install libssl-dev ./bootstrap -- -DCMAKE_BUILD_TYPE:STRING=Release make make install ``` ## Install DSSP > Info link: https://bio.tools/dssp > Manual: https://github.com/PDB-REDO/dssp/blob/trunk/doc/mkdssp.pdf ```bash git clone https://github.com/PDB-REDO/dssp.git cd dssp mkdir build export CXX=g++-9 export CC=gcc-9 sudo cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++-9 -DCMAKE_C_COMPILER=gcc-9 # Build files have been written to: /mnt/Tsunami_HHD/newloci/NativeEnsembleWeb_copy/dssp/build cmake --build build cmake --install build ``` Build ```bash sudo cmake --install build -- Install configuration: "Release" -- Installing: /usr/local/lib/libdssp.a -- Installing: /usr/local/lib/cmake/dssp/dsspTargets.cmake -- Installing: /usr/local/lib/cmake/dssp/dsspTargets-release.cmake -- Up-to-date: /usr/local/include/dssp.hpp -- Installing: /usr/local/lib/cmake/dssp/dsspConfig.cmake -- Installing: /usr/local/lib/cmake/dssp/dsspConfigVersion.cmake -- Installing: /usr/local/lib/pkgconfig/libdssp.pc -- Up-to-date: /usr/local/share/libcifpp/dssp-extension.dic -- Installing: /usr/local/bin/mkdssp -- Up-to-date: /usr/local/share/man/man1/mkdssp.1 ``` ## Install the [cif-tools](https://github.com/PDB-REDO/cif-tools) > Check it: https://github.com/PDB-REDO/cif-tools/issues/5#issuecomment-1774519022 ```bash= git clone https://github.com/PDB-REDO/cif-tools.git cd cif-tools mkdir build cd build export CXX=g++-9 export CC=gcc-9 sudo cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++-9 -DCMAKE_C_COMPILER=gcc-9 >>> -- Build files have been written to: /mnt/Tsunami_HHD/newloci/NativeEnsembleWeb_copy/cif-tools/build sudo cmake --build . sudo cmake --install . ``` After installation ```bash= -- Install configuration: "Release" -- Installing: /usr/local/bin/pdb2cif -- Installing: /usr/local/share/man/man1/pdb2cif.1 -- Installing: /usr/local/bin/cif2pdb -- Installing: /usr/local/share/man/man1/cif2pdb.1 -- Installing: /usr/local/bin/cif-diff -- Installing: /usr/local/share/man/man1/cif-diff.1 -- Installing: /usr/local/bin/cif-grep -- Installing: /usr/local/share/man/man1/cif-grep.1 -- Installing: /usr/local/bin/cif-merge -- Installing: /usr/local/share/man/man1/cif-merge.1 -- Installing: /usr/local/bin/cif-validate -- Installing: /usr/local/share/man/man1/cif-validate.1 -- Installing: /usr/local/bin/mmCQL -- Installing: /usr/local/share/man/man1/mmCQL.1 ``` ## Install [mrc](https://github.com/mhekkel/mrc) ```bash= git clone https://github.com/mhekkel/mrc.git cd mrc mkdir build cd build export CXX=/usr/bin/g++-9 cmake .. cmake --build . sudo cmake --install . ``` After installation ```bash= -- Install configuration: "" -- Installing: /usr/local/bin/mrc -- Installing: /usr/local/share/mrc/cmake/mrc-config.cmake -- Installing: /usr/local/share/man/man1/mrc.1 -- Installing: /usr/local/share/doc/mrc//example -- Installing: /usr/local/share/doc/mrc//example/CMakeLists.txt -- Installing: /usr/local/share/doc/mrc//example/mrc-user.cpp -- Installing: /usr/local/share/doc/mrc//example/hello.txt ``` ## Install [libcifpp](https://github.com/PDB-REDO/libcifpp) > Check it: https://github.com/PDB-REDO/libcifpp/issues/50 ```bash= git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules cd libcifpp export CXX=g++-9 export CC=gcc-9 cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release cmake --build build cmake --install build ``` Install libcifpp at /usr/local :::spoiler `cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release` ```bash= -- The CXX compiler identification is GNU 9.4.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++-9 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Not trying to recreate symop_table_data.hpp since CCP4 is not defined -- Performing Test GXX_LIBSTDCPP -- Performing Test GXX_LIBSTDCPP - Success -- Testing for known regex bug, since you're using GNU libstdc++ ... -- Build files have been written to: /mnt/Tsunami_HHD/newloci/NativeEnsembleWeb_copy/libcifpp/build ``` ::: :::spoiler `cmake --install build` ```bash= -- Install configuration: "Release" -- Installing: /usr/local/lib/libcifpp.a -- Installing: /usr/local/lib/cmake/cifpp/cifppTargets.cmake -- Installing: /usr/local/lib/cmake/cifpp/cifppTargets-release.cmake -- Installing: /usr/local/include/cif++ -- Installing: /usr/local/include/cif++/matrix.hpp -- Installing: /usr/local/include/cif++/item.hpp -- Installing: /usr/local/include/cif++/datablock.hpp -- Installing: /usr/local/include/cif++/forward_decl.hpp -- Installing: /usr/local/include/cif++/point.hpp -- Installing: /usr/local/include/cif++/parser.hpp -- Installing: /usr/local/include/cif++/pdb -- Installing: /usr/local/include/cif++/pdb/io.hpp -- Installing: /usr/local/include/cif++/pdb/cif2pdb.hpp -- Installing: /usr/local/include/cif++/pdb/pdb2cif.hpp -- Installing: /usr/local/include/cif++/pdb/tls.hpp -- Installing: /usr/local/include/cif++/dictionary_parser.hpp -- Installing: /usr/local/include/cif++/exports.hpp -- Installing: /usr/local/include/cif++/format.hpp -- Installing: /usr/local/include/cif++/gzio.hpp -- Installing: /usr/local/include/cif++/atom_type.hpp -- Installing: /usr/local/include/cif++/utilities.hpp -- Installing: /usr/local/include/cif++/iterator.hpp -- Installing: /usr/local/include/cif++/symmetry.hpp -- Installing: /usr/local/include/cif++/model.hpp -- Installing: /usr/local/include/cif++/category.hpp -- Installing: /usr/local/include/cif++/file.hpp -- Installing: /usr/local/include/cif++/row.hpp -- Installing: /usr/local/include/cif++/condition.hpp -- Installing: /usr/local/include/cif++/validate.hpp -- Installing: /usr/local/include/cif++/pdb.hpp -- Installing: /usr/local/include/cif++/text.hpp -- Installing: /usr/local/include/cif++/compound.hpp -- Installing: /usr/local/include/cif++.hpp -- Installing: /usr/local/share/libcifpp/mmcif_ddl.dic -- Installing: /usr/local/share/libcifpp/mmcif_pdbx.dic -- Installing: /usr/local/share/libcifpp/mmcif_ma.dic -- Installing: /usr/local/share/libcifpp/components.cif -- Installing: /usr/local/lib/cmake/cifpp/cifppConfig.cmake -- Installing: /usr/local/lib/cmake/cifpp/cifppConfigVersion.cmake -- Installing: /usr/local/etc/cron.weekly/update-libcifpp-data -- Installing: /usr/local/var/cache/libcifpp -- Installing: /usr/local/etc/libcifpp/cache-update.d -- Installing: /usr/local/etc/libcifpp.conf A configuration file has been written to /usr/local/etc/libcifpp.conf, please edit this file to enable automatic updates ``` ::: ## [Rhapsody](https://github.com/prody/rhapsody) or [Rhapsody](https://github.com/luponzo86/rhapsody) Installation, please refer to github website (python≤3.9) ```bash= # Take as your reference pip install -U prody-rhapsody # We also can download the folder git clone https://github.com/prody/rhapsody.git cd rhapsody pip install -e . ``` ```python import rhapsody as rd import os rd.initialSetup('./initialSetup') os.chdir('./initialSetup/') # Change working dir # Mapping SAV into PDB structure SAV_coord = ['P06213 906 A G'] rd.Uniprot.mapSAVs2PDB(SAV_coord) ``` ```bash= # Print out on your screen should be like this array([('P06213 906 A G', 'P06213 906 A G', '7PG0 A 867 A', 786)], dtype=[('orig. SAV coords', '<U25'), ('unique SAV coords', '<U25'), ('PDB SAV coords', '<U100'), ('PDB size', '<i4')]) ``` You then install a visualization software (e.g., VMD, PyMOL) to take a look at this mutation. - UniProtID: P06213 - PDB ID: 7PG0 - PDB chainID: A - PDB resID: 867 - Wild-type residue: A - Mutant residue: G ```python! # Generate features in Rhapsody study # 1. Total 33 features rhd = rd.Rhapsody(query=SAV_coord) rhd.setFeatSet('all') featMatrix = rhd.calcFeatures(filename=None) # 2. 8 features used in TANDEM-DIMPLE rhd.setFeatSet(['wt_PSIC', 'Delta_PSIC', 'BLOSUM', 'entropy', 'ranked_MI', 'ANM_effectiveness-chain', 'ANM_sensitivity-chain', 'stiffness-chain']) featMatrix = rhd.calcFeatures(filename=None) # Feature set rhd.featSet ``` ## Github 1. Setup SSH for GitHub repository https://docs.github.com/en/authentication/connecting-to-github-with-ssh/about-ssh 2. git push ```bash= git remote set-url origin git@github.com:locitran/locitran.github.io.git git remote -v # it should show following origin git@github.com:Loci-Tran/locitran.github.io.git (fetch) origin git@github.com:Loci-Tran/locitran.github.io.git (push) git push -u origin main # Since you modify your file and wanna update it on github git status # Check any files are modified or staged git add . # Stage your changes git add index.html # Stage a specific file rm -f .git/index.lock # Remove the .lock file if needed git commit -m "Updated index.html" git push -u origin main # Free jekyllthemes https://www.youtube.com/watch?v=qZsgPgGdOzQ ``` ## Github pages ```bash= # ruby and gem are installed in Mac: Defaults ruby -v gem -v gem install jekyll bundler ``` ## A100 ```bash= squeue sresource -u sresource -n ``` # Synchronize and Mount ```bash rsync -avzu --dry-run yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ tandem && \ rsync -aurtv tandem yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ rsync -avz --dry-run yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/test tandem rsync -hvrPt --dry-run yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ tandem # Sync only new/changed files ## From Hurricane to A100 rsync -hvrPt yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ ~/tandem/ ## From A100 to Hurricane rsync -hvrPt ~/tandem/ yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ # --dry-run to see the files will be transfered rsync -hvrPt --dry-run yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ ~/tandem/ sshpass -p Quangloc123 rsync -hrPt ~/tandem/ yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ && \ sshpass -p Quangloc123 rsync -hrPt yang_loci@140.114.97.192:/mnt/nas_1/YangLab/loci/tandem/ ~/tandem/ ``` | Column 1 | Column 2 | | -------- | -------- | | `-a` | Archive mode (preserves permissions, timestamps, symbolic links, etc.) | | `-v` | Verbose mode (shows progress) | | `-z` | Compress data during transfer (reduces bandwidth) | | `--progress` | Shows detailed progress during sync | | `-u` | Skips identical files (same timestamp and size). | Option Description -a -v Verbose mode (shows progress) -z Compress data during transfer (reduces bandwidth) --progress Shows detailed progress during sync To setup synchronizing two directories: ```bash # Add to ~/.bashrc file ## Sync both sites each 1 minute nohup bash -c 'while true; do echo "$(date "+%Y-%m-%d %H:%M:%S") Running sync_rsync.sh" >> $HOME/sync_rsync.log; /bin/bash $HOME/sync_rsync.sh; sleep 60; done' >> $HOME/sync_rsync.log 2>&1 & # sync_rsync.log 2025-03-08 13:49:19 Running sync_rsync.sh sending incremental file list... ``` # [TensorFlow](https://www.tensorflow.org/install/pip) running on GPU and [Pytorch](https://pytorch.org/) Take a look at this [site](https://www.tensorflow.org/install/source) to see which python/cuda version is available for GPU ## Installation ```bash! conda create --name tf python=3.9 conda activate tf python3 -m pip install tensorflow[and-cuda] # Verify the installation: python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))" ``` For testing Pytorch running on GPU, we do similarly ```bash! import torch torch.__version__() # '2.6.0+cu124' torch.cuda.is_available() # True torch.cuda.device_count() # 4 torch.cuda.current_device() # 0 torch.cuda.device(0) <torch.cuda.device at 0x7efce0b03be0> torch.cuda.get_device_name(0) # 'NVIDIA GeForce RTX 3080' # Set device device = torch.device('cuda' if torch.cuda.is_available() else 'cpu') print('Using device:', device) # Additional Info when using cuda if device.type == 'cuda': print(torch.cuda.get_device_name(0)) print('Memory Usage:') print('Allocated:', round(torch.cuda.memory_allocated(0)/1024**3,1), 'GB') print('Cached: ', round(torch.cuda.memory_reserved(0)/1024**3,1), 'GB') ``` ## Docker images for: [pytorch:2.6.0-cuda12.6-cudnn9-devel](https://hub.docker.com/layers/pytorch/pytorch/2.6.0-cuda12.6-cudnn9-devel/images/sha256-faa67ebc9c9733bf35b7dae3f8640f5b4560fd7f2e43c72984658d63625e4487) # Essential System Dependencies ## 1. Docker

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