Thang's Notes: Toolset

1. Cmake

need C++ compiler to install CMAKE, so need to load C++ compiler before install

Compile from source and install
https://github.com/Kitware/CMake/releases
Download CMake from: https://cmake.org/download/
wget https://cmake.org/files/v3.20/cmake-3.20.3.tar.gz

tar zxvf cmake-3.21.2.tar.gz

cd cmake-3.21.2
module load compiler/gcc-10.3
# USC 2:

./configure --prefix=/home1/p001cao/local/app/tool_dev/cmake-3.20.3

# USC 1:

./configure --prefix=/uhome/p001cao/local/app/tool_dev/cmake-3.21

make -j8

make install

create module file
cd /uhome/p001cao/local/Imodfiles

create file "cmake-3.17.2"

# for Tcl script use only

set topdir /uhome/p001cao/local/app/tool_dev/cmake-3.18.0

set version cmake-3.18.0

setenv cmake $topdir

prepend-path PATH $topdir/bin

Validate installation
module load cmake-3.17.2
cmake --version

Ref:
https://pachterlab.github.io/kallisto/local_build.html

https://github.com/Kitware/CMake

2. Autoconf (+lib)

https://www.gnu.org/software/autoconf/

ftp://alpha.gnu.org/pub/gnu/autoconf/
http://ask.xmodulo.com/upgrade-autoconf-centos.html
wget ftp://ftp.gnu.org/gnu/autoconf/autoconf-2.69b.tar.gz
tar zxf autoconf-2.69b.tar.gz

cd autoconf-2.69b


./configure --prefix=/home1/p001cao/local/app/tool_dev/autoconf-2.69b

2a. automake:

module load tool_dev/autoconf-2.69b

wget http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz
tar xvzf automake-1.14.tar.gz
cd automake-1.14
./configure --prefix=/home1/p001cao/local/app/tool_dev/automake-1.14

2b. update pkg-config (optional)
https://pkg-config.freedesktop.org/releases/?C=M;O=D
tar xvzf pkg-config-0.29.2.tar.gz
cd pkg-config-0.29.2
./configure --prefix=/home1/p001cao/local/app/tool_dev/pkg-config-0.29

2c. libtool:

https://www.gnu.org/software/libtool/

git clone git://git.savannah.gnu.org/libtool.git

##--
wget http://ftp.jaist.ac.jp/pub/GNU/libtool/libtool-2.4.6.tar.gz
tar xvfz libtool-2.4.6.tar.gz
cd libtool-2.4.6
./configure --prefix=/home1/p001cao/local/app/tool_dev/libtool-2.4.6

### use
export ACLOCAL_PATH=/home1/p001cao/local/app/tool_dev/libtool-2.4.6/share/aclocal

2d. autogen: (may not need)
2d1. Guile:
https://www.gnu.org/software/guile/manual/html_node/Obtaining-and-Installing-Guile.html
wget ftp://ftp.gnu.org/gnu/guile/guile-3.0.4.tar.gz
tar xvf guile-3.0.4.tar.gz
cd guile-3.0.4
module load compiler/gcc-10.2
module load tool_dev/libtool-2.4.6

./configure --with-libltdl-prefix=/home1/p001cao/local/app/tool_dev/libtool-2.4.6 \
--prefix=/home1/p001cao/local/app/tool_dev/guile-3.0.4

2d2. autogen:
wget https://ftp.gnu.org/gnu/autogen/rel5.18.16/autogen-5.18.16.tar.gz
tar xvfz autogen-5.18.16.tar.gz
cd autogen-5.18.16

./configure --prefix=/home1/p001cao/local/app/tool_dev/autogen-5.18.16

II. lld

1. https://lld.llvm.org/getting_started.html

cd Tooldev

git clone https://github.com/llvm/llvm-project.git llvm-master

cd llvm-master
mkdir build && cd build

module load tool_dev/cmake-3.17.2

module load conda/py37clangSupp

module load compiler/gcc-10.2
export myGCC=/home1/p001cao/local/app/compiler/gcc-10.2/bin

cmake ../llvm -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release \
-DLLVM_ENABLE_PROJECTS=lld \
-DCMAKE_CXX_COMPILER=${myGCC}/g++ -DCMAKE_C_COMPILER=${myGCC}/gcc \
-DCMAKE_INSTALL_PREFIX=/home1/p001cao/local/app/llvm/llvm-master-gcc10

2. lld may available with intel compiler

III. libxml2: (can use conda instead)

http://jianghao.wang/post/2017-11-07-install-packages-on-hpc/#install-libxml2

wget ftp://xmlsoft.org/libxml2/libxml2-2.9.9.tar.gz tar zxf libxml2-2.9.9.tar.gz cd libxml2-2.9.9 ./configure --prefix=/home1/p001cao/local/app/tool_dev/libxml2-2.9.9 --without-python

make make install

#--
prepend-path PKG_CONFIG_PATH $topdir/lib/pkgconfig

4. Update glibc

https://www.programmersought.com/article/32924660480/

strings /lib64/libc.so.6|grep GLIBC

http://www.gnu.org/software/libc/ # for all versions.

wget http://ftp.gnu.org/gnu/glibc/glibc-2.18.tar.gz # may error with other version, need root
tar xvf glibc-2.18.tar.gz
cd glibc-2.18

mkdir build && cd build

../configure --disable-profile --enable-add-ons \
--with-binutils=/home1/p001cao/local/app/tool_dev/binutils-2.32 \
--prefix=/home1/p001cao/local/app/tool_dev/glibc-2.18

ln -s /home1/p001cao/local/app/tool_dev/glibc-2.17/libc.so.6 /lib64/libc.so.6

check:  ldd --version

##NOTE:

https://www.jertype.com/posts/upgrading-glibc/

https://stackoverflow.com/questions/847179/multiple-glibc-libraries-on-a-single-host/52454603

export LD_LIBRARY_PATH=/home1/p001cao/local/app/tool_dev/glibc-2.15/lib:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/usr/local/lib

## Module file (not work)

if { [module-info mode load] || [module-info mode switch2] } {
    puts stdout "export LD_LIBRARY_PATH=/home1/p001cao/local/app/tool_dev/glibc-2.19/lib:$LD_LIBRARY_PATH;"
    puts stdout "export LD_LIBRARY_PATH=/usr/local/lib;"
} elseif { [module-info mode remove] && ![module-info mode switch3] } {
    puts stdout "export LD_LIBRARY_PATH=/usr/local/lib;"
}

###

export myBinutils=/home1/p001cao/local/app/tool_dev/binutils-2.32
--with-binutils=${myBinutils}

## use

export myGLIBC=/home1/p001cao/local/app/tool_dev/glibc-2.15/lib
LDFLAGS="-L${myGLIBC} -Wl,-rpath,${myGLIBC} -Wl,--dynamic-linker,${myGLIBC}/ld-linux-x86-64.so.2" \

Ref
https://stackoverflow.com/questions/35616650/how-to-upgrade-glibc-from-version-2-12-to-2-14-on-centos
https://www.gnu.org/software/libc/manual/html_node/Configuring-and-compiling.html
https://stackoverflow.com/questions/847179/multiple-glibc-libraries-on-a-single-host

4.1. musl libc (glibc alternative)

https://musl.libc.org/

tar xvf musl-1.2.0.tar.gz
cd musl-1.2.0

mkdir build && cd build

../configure --prefix=/home1/p001cao/local/app/tool_dev/musl-1.2.0

6. GSL

* need to link LAPACK, BLAS library when install Plumed in Lammps (but no need now)

https://coral.ise.lehigh.edu/jild13/2016/07/11/hello/

wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.6.tar.gz

./configure --prefix=/home1/p001cao/local/app/tool_dev/gsl-2.6

B. linker

Use conda to manager linker

module load conda/conda3

conda create -n py37linker python=3.7

#--

prepend-path PKG_CONFIG_PATH $topdir/lib/pkgconfig

#--
source activate py37linker

conda install autoconf automake cmake ninja libtool # make tool

conda install -c conda-forge lld=9.0.1 binutils # llmv & gold linker
conda install -c conda-forge numactl-devel-cos6-x86_64 # numa openmp

conda install -c asmeurer glibc
##--

LDFLAGS="-fuse-ld=lld -lrt"

Thang's Notes

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Wednesday, May 6, 2020

Toolset_dev