A Massively Spiffy Yet Delicately Unobtrusive Compression Library
Prerequisites
GNU 6.5
Compiling
wget http://www.zlib.net/zlib-1.2.11.tar.gz tar -xvzf zlib-1.2.11.tar.gz cd zlib-1.2.11 ./configure --prefix=/usr/local/zlib-1.2.11-gcc6 make check
Application
Test Failed… does not support .pth files
If you are doing a setup.py with specific directories
python setup.py install --prefix=/home/user1
If you are getting a PythonPath Error something like this.
TEST FAILED: /home/user1/lib/python3.7/site-packages/ does NOT support .pth files error: bad install directory or PYTHONPATH You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /home/user1/lib/python3.7/site-packages/ and your PYTHONPATH environment variable currently contains:
You can solve like by putting in your .bashrc.
export PYTHONPATH="${PYTHONPATH}:/home/user1/lib/python3.7/site-packages/"
source ~/.bashrc
Installing SCons-3.1.2 with Intel Python Distribution
What is SCons?
SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software.
For more information, see https://scons.org/
Prerequisites
Python 3 Distribution. For this I used the Intel Python Distribution
Get the Source Code
git clone https://github.com/SCons/scons.git
Setup scons directory and run the setup script
cd $HOME/scons /usr/local/intel/2020/intelpython3/bin/python setup.py install
Do note that the scons will write a site package at /usr/local/intel/2020/intelpython3/lib/python3.7/site-packages/SCons-3.9.9a993-py3.7.egg . You need to allow the necessary permission
Testing the package
cd /usr/local/scons
python runtest.py SCons/BuilderTests.py
1/1 (100.00%) /usr/local/intel/2020/intelpython3//bin/python SCons/BuilderTests.py ...................................... ---------------------------------------------------------------------- Ran 38 tests in 0.096s OK
References:
Compiling Gromacs-2019.3 with Intel MKL and CUDA
Prerequisites
GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3
Intel Compilers and Prerequisites
source /usr/local/intel/2018u3/bin/compilervars.sh intel64 source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64 source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64 source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64 MKLROOT=/usr/local/intel/2018u3/mkl
Create a setup file
touch gromacs_cpu.sh
Put the following into the gromacs_cpu.sh
CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" -DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" -DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install
Testing and Verification
$ source /your/installation/prefix/here/bin/GMXRC ./gmxtest.pl all -np 2
Compiling Gromacs-2019.3 with Intel 2018 and MKL
Prerequisites
GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3
Intel Compilers and Prerequisites
source /usr/local/intel/2018u3/bin/compilervars.sh intel64 source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64 source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64 source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64 MKLROOT=/usr/local/intel/2018u3/mkl
Create a setup file
touch gromacs_cpu.sh
Put the following into the gromacs_cpu.sh
CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" -DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" -DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install
Testing and Verification
$ source /your/installation/prefix/here/bin/GMXRC ./gmxtest.pl all -np 2
G16NBO is currently configured with only 100000000 words Errors
If you encounter errors when you use NBO7 with Gaussian G16a
This calculation is attempting to allocate 299857248 words of scratch memory, but G16NBO is currently configured with only 100000000 words. If you have the NBO6 source distribution, you can reconfigure G16NBO by editing maxmem.fh in nbo6/src/g16nbo/include and rebuilding the executables.
Dynamic memory allocation in the GenNBO, G09NBO, and G16NBO interfaces to NBO7 has been implemented. The issue has been fixed with the latest download from NBO7 site.
Remember to update gennbo.sh at your NBO directory
# Examples: # setenv NBOMEM 50mw # setenv NBOMEM 512mb # setenv NBOMEM 1gb setenv NBOMEM 1gb
References:
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Introduction to Healthcare Series
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Bridging the Gap between Engineering and Healthcare
26 May 2002:00 – 02:30 pm (SGT)
Bridging the Gap: How to Translate the Reality into The Computer Language
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Can’t execute `conda activate` from bash script
I am still new to Anaconda and I encountered this error
"Can't execute conda activate from bash script"
To resolve the issue was pretty fast. I took a look at https://github.com/conda/conda/issues/7980
source ~/anaconda3/etc/profile.d/conda.sh conda activate my_env
Solving environment: failed with initial frozen solve. Retrying with flexible solve
When I was loading my anaconda-2020, I’ve received this error.
conda install -c conda-forge opencv
And I got this error
Solving environment: failed with initial frozen solve. Retrying with flexible solve....
There was this thread from github which was useful and it help a lot! https://github.com/conda/conda/issues/9367
Step 1: To resolve, Create an environment called opencv using
conda create -n opencv
Step 2: Activate it
conda activate opencv
Step 3: Install it again
conda install -c anaconda opencv
(which install opencv 3, but not the most recent 4. In order to create a second environment called opencv4. Use above code to create and activate and do a standard download:
conda install -c conda-forge opencv
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