安装脉冲星相关软件 | Pulsar software installation

本文假定安装软件到 $PREFIX, 比如 PREFIX=/opt/$NAME. 当然也可将不同软件安装到同一目录, 例如 PREFIX=$HOME/pulsar_software. 以下内容中请把 $PREFIX 替换为你想要的值.
This article assumes installing software into $PREFIX, e.g. PREFIX=/opt/$NAME. Of course you can install into same directory, e.g. PREFIX=$HOME/pulsar_software. Please replace $PREFIX with the value you want in the following content.

本文以类 Debian 环境为例, 使用其他包管理器的用户可自行搜索软件包名. 对于 RHEL, 通常 -dev -> -devel.
This article uses Debian-like environment. Users with other package managers may search for package name by yourself. For RHEL, usually -dev -> -devel.

如有任何问题或评论, 可在 https://github.com/fxzjshm/fxzjshm.github.io/issues 提出.
If you have any question or comment, consider post it at https://github.com/fxzjshm/fxzjshm.github.io/issues.

相关环境变量 | Useful environment variables

• PATH
• LD_LIBRARY_PATH
• LIBRARY_PATH
• CPATH

构建需要的软件 | Dependencies of building

要编译软件, 显然需要编译器, 这里以 gcc 与 gfortran 为例.
To compile software apparently compilers are required. Here gcc and gfortran is used as example.

sudo apt install gcc gfortran g++

很多软件的构建系统是 Autoconf 和 CMake, 所以需要先安装好它们以便正确配置构建脚本.
Many of these software uses Autoconf or CMake as building system, so these need to be installed so that it can configure build script properly.

sudo apt install autoconf cmake

PGPLOT

• https://sites.astro.caltech.edu/~tjp/pgplot/
• 简而言之: 不要自己编译 PGPLOT. 用软件源里的版本.
  TL;DR: Don’t build PGPLOT. Use package from distro.

Debian-like

sudo apt install pgplot5

如果没找到, 可能需要在 /etc/apt/sources.list 中启用 non-free (Debian) / multiverse (Ubuntu):
If not found, you may need to enable non-free (Debian) / multiverse (Ubuntu) in /etc/apt/sources.list:

- deb http://mirrors.pku.edu.cn/debian/ bookworm main
+ deb http://mirrors.pku.edu.cn/debian/ bookworm main contrib non-free

- deb https://mirrors.pku.edu.cn/ubuntu/ jammy main
+ deb https://mirrors.pku.edu.cn/ubuntu/ jammy main restricted universe multiverse

因为 PGPLOT 按定义不是 “自由软件”.
because PGPLOT is not “free software” by definition.

RHEL-like

RHEL 8 & 9 官方软件源中没有 PGPLOT.
There’s no PGPLOT in official repo as of RHEL 8 & 9.

考虑在第三方软件源中搜索 PGPLOT (比如 https://pkgs.org/search/?q=pgplot), 风险自担.
Consider searching third-party repo for PGPLOT (e.g. https://pkgs.org/search/?q=pgplot) and use it at your own risk.

Tempo

• https://tempo.sourceforge.net/

git clone https://git.code.sf.net/p/tempo/tempo
cd tempo

# 注意到 prepare 脚本使用 csh, 而大部分系统中并不预装 csh, 故直接执行对应命令即可
# noticed that "prepare" uses csh which isn't pre-installed in most systems, so just run command inside
autoreconf --install

./configure --prefix=$TEMPO_PREFIX

# 使用 autoconf 产生的 Makefile 编译, -j 选项用于并行编译, nproc 给出机器的 CPU 核心数, 也可以手动指定
make -j`nproc`
# 安装到 $PREFIX
make install -j`nproc`

PRESTO

• https://github.com/scottransom/presto

参考仓库中的 INSTALL.md.
Refer to INSTALL.md in repo.

安装依赖项: PGPLOT, FFTW 3, GLib 2, cfitsio.
Install dependencies: PGPLOT, FFTW 3, GLib 2, cfitsio.

sudo apt install pgplot5 libfftw3-dev libglib2.0-dev libcfitsio-bin libcfitsio-dev

安装构建工具 meson. 这里直接使用了软件源, 一些人可能认为在虚拟环境中安装更好.
Install building system used: meson. Here OS repo is used, some people prefer installing in Python virtual environment.

sudo apt install meson

然后开始构建.
Then start building.

git clone https://github.com/scottransom/presto
cd presto
export PRESTO=`pwd`
export TEMPO=$TEMPO_PREFIX
meson setup build --prefix=$PRESTO_PREFIX
# 可能会要求安装更多依赖项, 比如
# may require installing more dependencies like: 
#          libx11-dev linpng-dev

python3 check_meson_build.py
# 可能要求设置环境变量, 例如
# may require setting environment variables, e.g.
#export PATH=$PRESTO_PREFIX/bin:$PATH
#export LIBRARY_PATH=$PRESTO_PREFIX/lib/riscv64-linux-gnu:$LIBRARY_PATH
#export LD_LIBRARY_PATH=$PRESTO_PREFIX/lib/riscv64-linux-gnu:$LD_LIBRARY_PATH
# 可将这些总结到 env.sh 中以备以后调用
# you may write these into env.sh to be sourced when later used

meson compile -C build
meson install -C build

cd python
# 在给 presto 使用的 Python 虚拟环境中
# in Python virtual environment used for presto
pip install --config-settings=builddir=build . 

PSRCHIVE + DSPSR

• https://psrchive.sourceforge.net/index.shtml
• https://dspsr.sourceforge.net/

Tempo2

• https://bitbucket.org/psrsoft/tempo2

PulsarX + TransientX

以安装到 $PULSARX_PREFIX 为例.
Assume installing to $PULSARX_PREFIX.

安装依赖项:
Install dependencies:

sudo apt install libboost-all-dev libtool liblapack-dev

注意 libboost-dev 不足以完整安装 Boost 库.
Notice that libboost-dev is not enough for a full Boost installation.

另外, 还需安装 tempo2, 并需要添加到 PATH.
Moreover, tempo2 also need to be installed and added to PATH.

YMW16 是可选的, 安装之后需要设置 YMW16_DIR.

以下假定将 PlotX, XLibs, PulsarX, TransientX 安装到 PULSARX_PREFIX, 比如 /opt/PulsarX.
Here assumes installing PlotX, XLibs, PulsarX, TransientX into PULSARX_PREFIX, e.g. /opt/PulsarX.

在目标文件夹下创建 env.sh 之类的文件并在运行之前 source 这个文件来自动调整 PULSARX_PREFIX, 设置其他软件的路径同理.
Create file like env.sh inside target directory and source it before executing other commands to automatically adjust PULSARX_PREFIX. Paths of other software can also be set like this.

PulsarX 和 TransientX 有可能不能找到它们的依赖项 (XLibs, PlotX 等), 故用 CPATH 和 LIBRARY_PATH 来绕过这个问题.
Configure scripts of PulsarX & TransientX may not find its dependencies (XLibs, PlotX, etc.), so CPATH and LIBRARY_PATH is used as a workaround:

# in $PULSARX_PREFIX/env.sh, e.g. /opt/PulsarX/env.sh
export PULSARX_PREFIX="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

export PATH=$TEMPO2_PREFIX/bin:$PATH

export CPATH=$PULSARX_PREFIX/include:$CPATH
export LIBRARY_PATH=$PULSARX_PREFIX/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$PULSARX_PREFIX/lib:$LD_LIBRARY_PATH
export PATH=$PULSARX_PREFIX/bin:$PATH

# before using other commands: 
source /opt/PulsarX/env.sh  # or in target path you choose

开始构建, 参考命令:
Start building. Example command:

git clone https://github.com/ypmen/XLibs
git clone https://github.com/ypmen/PlotX
git clone https://github.com/ypmen/TransientX
git clone https://github.com/ypmen/PulsarX

cd XLibs
./bootstrap
./configure --prefix=$PULSARX_PREFIX
make -j`nproc`
make install -j`nproc`
cd ..

cd PlotX
./bootstrap
./configure --prefix=$PULSARX_PREFIX
make -j`nproc`
make install -j`nproc`
cd ..

cd TransientX
./bootstrap
./configure --prefix=$PULSARX_PREFIX
make -j`nproc`
make install -j`nproc`
cd ..

cd PulsarX
./bootstrap
./configure --prefix=$PULSARX_PREFIX
make -j`nproc`
make install -j`nproc`
cd ..

注意 configure 的报错很多情况下并不准确, 请查看 config.log 来确定真实原因.
Notice that error from configure isn’t accurate, refer to config.log for real situation.
例如, “checking PGPLOT installation… library not found!” 的真实原因是:
For example, “checking PGPLOT installation… library not found!” is actually caused by:

# in config.log
configure:16966: checking PGPLOT installation
configure:16983: gcc -o conftest -g -O2   conftest.c -lcpgplot -lpgplot -lcfitsio -lpng  -lgfortran -lm -lquadmath -lX11 >&5
/usr/bin/ld: cannot find -lquadmath: No such file or directory
collect2: error: ld returned 1 exit status
configure:16983: $? = 1

注意 PulsarX 中的构建配置对新版本 Python 缺少支持, 需要手动修改, 见 https://github.com/ypmen/PulsarX/pull/5.
Notice that build config in PulsarX lacks support for new versions of Python, need to be manually patched. See https://github.com/ypmen/PulsarX/pull/5.

diff --git a/config/ax_python.m4 b/config/ax_python.m4
index 05efd1c..2ea0355 100644
--- a/config/ax_python.m4
+++ b/config/ax_python.m4
@@ -55,7 +55,7 @@
 AC_DEFUN([AX_PYTHON],
 [AC_MSG_CHECKING(for python build information)
 AC_MSG_RESULT([])
-for python in python3.8 python3.7 python3.6 python3.5 python3.4 python3.3 python3.2 python3.1 python3.0 python2.7 python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python; do
+for python in python3.13 python3.12 python3.11 python3.10 python3.9 python3.8 python3.7 python3.6 python3.5 python3.4 python3.3 python3.2 python3.1 python3.0 python2.7 python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python; do
 AC_CHECK_PROGS(PYTHON_BIN, [$python])
 ax_python_bin=$PYTHON_BIN
 if test x$ax_python_bin != x; then

若出现找不到 boost_system 相关的库 (在 Ubuntu 18.04 上有报道), 可在 configure.ac 中加入 -lboost_system:
If cannot find symbols from boost_system (reported in Ubuntu 18.04), may add -lboost_system in configure.ac:

diff --git a/configure.ac b/configure.ac
index 1e9ba79..61e788e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -16,7 +16,7 @@ CXXFLAGS='-std=c++11 -O3'
 LT_INIT
 
 # Checks for libraries.
-AX_BOOST_BASE([1.56], [LIBS="$LIBS -lboost_program_options -lboost_log"], [echo "Boost library was not found!";exit -1])
+AX_BOOST_BASE([1.56], [LIBS="$LIBS -lboost_program_options -lboost_log -lboost_system"], [echo "Boost library was not found!";exit -1])
 AC_CHECK_LIB([cfitsio], [ffgky], [], [echo "cfitsio library was not found!";exit -1])
 AC_CHECK_LIB([png], [png_set_flush], [], [echo "library not found!";exit -1])
 AC_CHECK_LIB([fftw3], [fftw_malloc], [], [echo "library not found!";exit -1])