FFTW Library

Optimization Solution:

1. Open the Makefile-linux-cpu file.
2. Locate the LIBS section in the file.
3. Add $(LIBPLUMED) before $(LIBFFTW) in the LIBS line:

LIBS = $(LIBPLUMED) $(LIBFFTW) ...

4. This adjustment ensures that the PLUMED library is linked correctly before FFTW.
5. Save the changes and re-run the compilation process.

Plumed Library

Optimization Solution:

1. Set the PLUMED_ROOT environment variable:
   export PLUMED_ROOT=<path>/third-party/plumed-2.9.2
2. Update the PATH environment variable:
   export PATH=$PLUMED_ROOT/bin:$PATH
3. Update the LD_LIBRARY_PATH environment variable:
   export LD_LIBRARY_PATH=$PLUMED_ROOT/lib:$LD_LIBRARY_PATH
4. Set the PLUMED_PATCHES environment variable:
   export PLUMED_PATCHES=$PLUMED_ROOT/patches
   Note: The patches folder might be located in the plumed-src directory. If it is not found in the expected location, manually move it into the PLUMED_ROOT directory.

Optimization Solution:

1. Open the build.sh file.
2. Locate the FFTW build section.
3. Replace the following command:
   make -j${numCores} with: make CFLAGS=-fPIC -j${numCores}
4. Locate the Plumed build section.
5. Add the following environment variables before compiling PLUMED to specify the FFTW include and library paths:

export CPPFLAGS='-I/<path>/fftw-3.3.10/include'
export LDFLAGS='-L/<path>/fftw-3.3.10/lib'

6. Save the changes and re-run build.sh.

XTB Library

Optimization Solution:

1. Open the build.sh script.
2. Locate the section for initializing XTB.
3. Add the following Git commands before compilation:

git init
git config user.name "Your Name"
git config user.email "your.email@example.com"
git add .
git commit -m "Initial commit"

Optimization Solution:

1. Find the path to the LAPACK and BLAS libraries.
2. Modify the cmake command in build.sh:

-DLAPACK_LIBRARIES=<path>/liblapack.so
-DBLAS_LIBRARIES=<path>/libopenblas.so

3. Save the changes and re-run the build script.

Optimization Solution:

1. Ensure no other versions of XTB are included in your environment variables.
2. Run the following command to verify mctc-lib path:

grep -i "mctc-lib" build/CMakeCache.txt

3. The correct output path should be: ./xtb-6.5.0-src/subprojects/mctc-lib
4. If incorrect, adjust and recompile.

DL-FIND Library

Optimization Solution:

1. Open the Makefile.qbics file.
2. Locate the gfortran compiler section and uncomment the -fallow-argument-mismatch option.
3. Save the file and recompile the code.

##  gfortran (gcc) compiler
-
-
-
F90FLAGS   =   -fimplicit-none  -fbounds-check -std=gnu -Wconversion \
-Wsurprising -fallow-argument-mismatch

4. If this does not resolve the issue, try using -Wno-argument-mismatch instead.

Optimization Solution:

1. Open the Makefile in the qbics-source folder.
2. In the LIBS section, place $(LIBDLFIND) before $(LIBBLAS).
3. Save the Makefile and recompile Qbics.

OpenBLAS Library

Optimization Solution:

1. Open the build.sh file.
2. Locate the section where OpenBLAS is compiled.
3. Modify the following line:

make TARGET=HASWELL -j${numCores}

4. Save the changes and recompile the project.

Memory

Optimization Solution:

1. For third-party libraries (e.g., PLUMED):
2. Open the build.sh script.
3. Add the following line to the PLUMED section:

export CXXFLAGS="-O1"

4. Remove the -j${numCores} option from the make command.
5. Save the changes and re-run the compilation.
6. For Qbics compilation:
7. Open the Makefile-linux-cpu file.
8. Change -O2 to -O1 in the CXXFLAG setting.
9. Save the file and recompile to reduce memory usage.

System Architecture Compatibility

Optimization Solution:

1. Open the Makefile file.
2. Locate the CXXFLAG section and adjust flags according to your system architecture:
3. Case One: If the output indicates:

./build/linux-cpu/obj/dft/GrimmeDFTD_Link.o: ELF 64-bit LSB relocatable, x86-64, version 1 (SYSV), not stripped

Add -march=armv8-a at the end of the CXXFLAG line.
4. Case Two: If the error message is:

g++: error: unrecognized command line option '-mavx2'
g++: error: unrecognized command line option '-mfma'

Then remove -mavx2 -mfma from CXXFLAG.
5. Save the changes and re-run the compilation process.

Locate and Replace the Path of Intel OneAPI

Optimization Solution:

1. Check whether the Intel compiler is installed. If it returns a valid path, skip to Step 3.

   which icc

2. Load the Intel Compiler Module:
   • Check for available Intel modules:

   module avail

   • Load the module if available:

   module load <intel_module_name>

   • Add the load command to .bashrc or .bash_profile for persistence.
   • If unavailable, contact the system administrator or install the Intel OneAPI toolkit manually.
3. Locate the Intel compiler installation directory:
   • Use which icc to find the executable.
   • From this path, locate the directory containing setvars.sh (commonly under /opt/intel/oneapi/).
4. Update build configuration files:
   • Open the build.sh script and replace the Intel path with the correct setvars.sh directory.
   • Also update Makefile-linux-cpu in the qbics-src directory to reflect the correct path.

setvars.sh Already Executed

Optimization Solution:

1. Open the build.sh script.
2. Locate the line where setvars.sh is sourced.
3. Add the --force flag to force re-execution of the script:

   source <path>/setvars.sh --force

Qbics Compilation: Missing mkl.h

Optimization Solution:

1. Navigate to the qbics-src directory.
2. Run the following command manually instead of using build.sh:

   make -f Makefile-linux-cpu

Third-Party Library Conflicts

Optimization Solution:

1. Method One: Clean and Rebuild
   1. Navigate to the Qbics root directory (e.g., ~/qbics-version).
   2. Execute the following command to remove old compiled objects:

      ./build.sh clean

   3. Then recompile everything by running:

      ./build.sh

2. Method Two: Verify Folder Names
   1. Check whether the compiled MKL (or other) libraries were installed under a folder named lib or lib64.
   2. Open the Makefile-linux-cpu file and update the library paths to match the actual folder name.

Running Qbics

Optimization Solution:

1. Before executing qbics-linux-cpu, re-source the Intel oneAPI environment:

   source <path>/setvars.sh

2. (Optional) Add the above source command to your shell environment file (e.g., ~/.bashrc or ~/.bash_profile).
   Note: This is recommended, but on certain servers, modifying environment files may interfere with file transfers. Use with caution.

Missing GSL Library

Optimization Solution:

1. Open the Makefile-linux-cpu file in the Qbics source directory.
2. Locate the LIBS section.
3. Add the following flags to the LIBS line:

   -lgsl -lgslcblas

4. Save the Makefile and recompile Qbics.

Input File Types

Optimization Solution:

1. Navigate to the directory containing the problematic file.
2. Run the following command to convert the file format:

   dos2unix XXX.xyz

3. dos2unix is a command-line tool used to convert Windows-style line endings (CRLF) into Unix-style (LF).

Calling the Plumed Library Alone

Optimization Solution:

1. Use the find command to locate the libplumedkernel.so file:

   find <path>/third-party/plumed-2.9.2 -name libplumedkernel.so

2. If the file is found, set the relevant environment variables:

   export PLUMED_ROOT=<path>/third-party/plumed-2.9.2
   export PATH=$PLUMED_ROOT/bin:$PATH
   export LD_LIBRARY_PATH=$PLUMED_ROOT/lib:$LD_LIBRARY_PATH
   export PLUMED_PATCHES=$PLUMED_ROOT/patches