General Installation and Usage Instructions

Please follow these instructions for a general deployment on Linux machines. There are a number of complications that can lead to failures when attempting to deploy this code for yourself, but this guide attempts to prescribe broad measures to avoid them. Because of the variability of different operating system environments, remedial actions cannot always be given for certain issues. A separate guide exists in purdue_install.md for users working at Purdue University to address their specific challenges.

Installation and Usage

Ensure that the following programs are installed on the machine by seeing if there is an output to each of the following commands in these categories:
- Selected package manager development tools
  - GNU Autoconf: which autoconf
  - GNU Automake: which automake
  - GNU Bison: which bison
  - Flex: which flex
  - GNU Compiler Collection (GCC version 7 or newer): which gcc, which g++, and which gfortran
  - GNU Make: which make
- Boost C++ Libraries (Boost version 1.57.0 or newer): locate "filtering_stream.hpp"
- CMake (CMake version 3.7.0 or newer): which cmake and cmake --version
- git: which git
- Intel Math Kernel Library (MKL): locate "mklvars.sh"
- Lemon: which lemon
- OpenMPI (OpenMPI version 4.0.1 or newer): which mpicc, which mpicxx
- Zlib (Zlib version 3.13 or newer): locate "zlib.h"
- If any of these programs are not installed, then it is recommended that someone with root access install whatever is missing using the package manager (most programs) or by building from source (GCC, Boost, and OpenMPI).
Clone this respository into your working location with git clone git@github.com:purdue-onchip/gds2Para.git
- If cloning fails, the usual reason is that a secure connection to the server could not be made. It is important to clone to be able to use git to receive updates. These steps will help get yourself going using git:
  1. Check if you have any public keys such as id_rsa.pub by running ls -lh .ssh in your home directory
  2. If no public keys appear, then generate one by running ssh-keygen -t rsa -C <email> in your home directory, where <email> is your work email address (note that this utility may not be available on all machines)
  3. The key generation command will require you to click "Enter" to place the public key in the default location, and then click "Enter" twice more to forgo additional password protection
  4. Open the public key id_rsa.pub in a text editor; for example, run vim ~/.ssh/id_rsa.pub
  5. In your GitHub account, go to your SSH and GPG keys under your account settings and click the green "New SSH key" button
  6. Give this SSH public key title such as "Work Network"
  7. Copy and paste the contents of id_rsa.pub open in the text editor verbatim into the key field
  8. Click the green "Add SSH key" button
  9. Navigate back to your working location and attempt to clone the repository again
- If cloning and SSH key generation fail, try to download the files by clicking the green "Clone or download" button on the Code tab of this repository followed by "Download ZIP"
  1. Move the zip archive to the working location
  2. Unzip the archive with unzip gds2Para-master.zip
  3. Rename the recently created directory from "gds2Para-master" to "gds2Para"
Clone the Limbo repository into your working location with git clone https://github.com/limbo018/Limbo.git
- If cloning fails, try to download the files by clicking the green "Clone or download" button on the Code tab of the Limbo repository followed by "Download ZIP"
  1. Move the zip archive to the working location
  2. Unzip the archive with unzip Limbo-master.zip
  3. Rename the recently created directory from "Limbo-master" to "Limbo"
Clone the Parser-SPEF repository into your working location with git clone https://github.com/OpenTimer/Parser-SPEF.git
- If cloning fails, try to download the files by clicking the green "Clone or download" button on the Code tab of the Parser-SPEF repository followed by "Download ZIP"
  1. Move the zip archive to the working location
  2. Unzip the archive with unzip Parser-SPEF-master.zip
  3. Rename the recently created directory from "Parser-SPEF-master" to "Parser-SPEF"
Clone the eigen-git-mirror repository into your working location with git clone https://github.com/eigenteam/eigen-git-mirror.git
- If cloning fails, try to download the files by clicking the green "Clone or download" button on the Code tab of the eigen-git-mirror repository followed by "Download ZIP"
  1. Move the zip archive to the working location
  2. Unzip the archive with unzip eigen-git-mirror-master.zip
  3. Rename the recently created directory from "eigen-git-mirror-master" to "eigen-git-mirror"
Ensure that you are the owner of the files that were downloaded with full read/write/execute permissions
- Change ownership with chown -R <username>:<username> <directory>, where <username> is your username and <directory> is each of "gds2Para/", "Limbo/", "Parser-SPEF/", or "eigen-git-mirror/"
- Change permissions with chmod -R 744 <directory>, where <directory> is each of "gds2Para/", "Limbo/", "Parser-SPEF/", or "eigen-git-mirror/"

Modify run commands files depending on the shell indicated by echo $SHELL, substituting <absolute path to C compiler> for a valid path to a C language compiler, <absolute path to C++ compiler>, for a valid path to a C++ compiler, <absolute path to Fortran compiler> for a valid path to a Fortran compiler, <absolute path to OpenMPI binaries> for a valid path to the OpenMPI binaries, <absolute path to OpenMPI static libraries> for a valid path to the OpenMPI static libraries, <absolute path to Boost directory> for a valid path to the Boost C++ headers directory, <absolute path to Limbo directory> for a valid path to the Limbo directory, <absolute path to Parser-SPEF directory> for a valid path to the Parser_SPEF directory, <absolute path to Eigen directory> for a valid path to the Eigen directory, <absolute path to future HYPRE directory> for a valid path to the HYPRE directory yet to be created, and <absolute path to MKL directory> for a valid path to the Intel Math Kernal Library (MKL) directory when it appears

For users of Trusted Silicon Stratus, the previous installation steps are completed for you, so edit the file ".bashrc" in your home directory by appending the following:

# Skip rest of file if not interactive
if [ -z "$PS1" ]; then
    return
fi

# User specific aliases and functions
source /opt/gds2Para_setup.sh

For "bash", edit the file ".bashrc" in your home directory by appending the following:

# Skip rest of file if not interactive
if [ -z "$PS1" ]; then
    return
fi

# Environment Variables for Compilers
export CC=<absolute path to C compiler>
export CXX=<absolute path to C++ compiler>
export FC=<absolute path to Fortran compiler>

# Environment Variables for OpenMPI
export OMPI_CC=$CC
export OMPI_CXX=$CXX
export OMPI_FC=$FC
export PATH=<absolute path to OpenMPI binaries>:$PATH
export LD_LIBRARY_PATH=<absolute path to OpenMPI static libraries>:$LD_LIBRARY_PATH

# Environment Variables for GDSII File Handling
export BOOST_DIR="<absolute path to Boost directory>"
export LIMBO_DIR="<absolute path to Limbo directory>"
export PARSER_SPEF_DIR="<absolute path to Parser-SPEF directory>"
export EIGEN_DIR="<absolute path to Eigen directory>"
export HYPRE_DIR="<absolute path to future HYPRE directory>"
export MKL_DIR="<absolute path to MKL directory>"

For "tcsh", edit the file ".cshrc" in your home directory by appending the following:

# Skip Rest of File if Not Interactive
if (! $?prompt) then
    exit 0
endif

# Environment Variables for Compilers
setenv CC <absolute path to C compiler>
setenv CXX <absolute path to C++ compiler>
setenv FC <absolute path to Fortran compiler>

# Environment Variables for OpenMPI
setenv OMPI_CC ${CC}
setenv OMPI_CXX ${CXX}
setenv OMPI_FC ${FC}
setenv PATH <absolute path to OpenMPI binaries>:${PATH}
setenv LD_LIBRARY_PATH <absolute path to OpenMPI static libraries>:${LD_LIBRARY_PATH}

# Environment Variables for GDSII File Handling
setenv BOOST_DIR <absolute path to Boost directory>
setenv LIMBO_DIR <absolute path to Limbo directory>
setenv PARSER_SPEF_DIR <absolute path to Parser-SPEF directory>
setenv EIGEN_DIR <absolute path to Eigen directory>
setenv HYPRE_DIR <absolute path to future HYPRE directory>
setenv MKL_DIR <absolute path to MKL directory>

Ensure that the compiler versions support the following standards: GNU Fortran (superset of F95) for Fortran, C99 for C language, and C++17 for C++.
It appears that Intel MKL-DNN for deep neural networks is not compatible with installation, only regular Intel MKL is

Exit the shell and terminate the connection before logging back in
Ensure that the run command files were properly loaded by running echo $LIMBO_DIR
- If nothing shows up for "bash" users, run cp .bashrc .bash_profile in the home directory, exit the shell, log back in, and try again
- If nothing shows up for "tcsh" users, run cp .cshrc .tcshrc in the home directory, exit the shell, log back in, and try again
- For all other errors, contact the primary maintainer
Enter the directory "Limbo" from the working location
Run git reset --hard 3.3.0 to revert to an earlier version of the repository
- The partial installation of Limbo components needed to run gds2Para is feasible only before CMake was introduced as the way to build the entirety of Limbo
- Only the necessary parsers will be built from Limbo using these instructions, and users wanting to use other Limbo features should follow the installation instructions given in that repository
- (Optional) It is believed that the necessary components and most other components of Limbo can be built using make in the top directory of Limbo following these instructions, but this has not been tested
Install third-party LEF & DEF readers by following the instructions in file /Limbo/limbo/thirdparty/lefdef/5.8/lefdefReadme.txt
Compile Limbo's parsers
- Limbo's GDSII parser: Enter the directory "/Limbo/limbo/parsers/gdsii/stream". Run make -j 2 in this directory to build certain Limbo libraries
- Limbo's LEF parser: Enter the directory "/Limbo/limbo/parsers/lef/adapt". Run make -j 2.
- Limbo's DEF parser: Enter the directory "/Limbo/limbo/parsers/def/adapt". Run make -j 2.
Ensure that new static libraries named libgdsparser.a, liblefparseradapt.a, and libdefparseradapt.a exist in directory "/Limbo/lib"
Follow the instructions in HYPRE Setup to prepare multigrid methods from HYPRE
- It is necessary to make all changes to ".bashrc" and ".cshrc" in the home directory before following these instructions
- Additional environment variables may need to be set depending on the setup of your Linux machine
- Continue following the remaining steps once HYPRE is installed
Enter the directory "gds2Para" from the working location
(Optional) Add more GDSII files to the directory "examples/" within the working location
- Some usage modes of this software may also require a simulation input file in a similar format to the preexisting examples (the file name before the suffix must match that of the GDSII file before ".gds")
- Files created from the software will be added directly to the present working directory by default
- The files optionally added may be used in place of the examples in the rest of the instructions
Run make in shell to compile executable LayoutAnalyzer
Run LayoutAnalyzer --help to get a list of the available control modes which the executable supports
Run LayoutAnalyzer -r examples/nand2.gds in shell to produce terminal output describing the GDSII file
Perform a complete parameter extraction by running mpirun LayoutAnalyzer -s examples/SDFFRS_X2.gds examples/SDFFRS_X2.sim_input examples/SDFFRS_X2.cir to read in the design and simulation input file, do all analysis, and return the results in a Xyce (SPICE-compatible) subcircuit
- It is necessary to use mpirun to guarantee memory integrity in the parallelized portions of the software.

HYPRE Setup

Clone the HYPRE repository into your working location with git clone https://github.com/hypre-space/hypre.git
- This requires the setup of an SSH key for a secure connection
Enter the directory "hypre/src/cmbuild" from the working location
- Configuration options may be viewed using ../configure --help
- The recommended installation involves CMake rather than the simpler, possible installation using only make and the included configure tool

Run cmake --version and ensure that the version of CMake installed is at least 3.7.0
Run cmake -LA .. and ensure that CMake found the correct versions of the compilers
- CMake is rather temperamental and tends to overlook common methods of specifying different compilers system-wide
- Check ".bashrc" or ".cshrc" in your home directory to see if the environment variables for the compilers are properly set
- In particular, the settings for OpenMPI are difficult to apply when building HYPRE except by paying very careful attention to these installation instructions
Run cmake .. to produce a makefile
Run make install -j 2 from within the same location ("hypre/src/cmbuild" in the working location) to install header files
Return to working directory and ensure that a new library file named HYPRE.h exists by running ls -lh hypre/src/hypre/include

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