update zmatlib, use miniz, drop zlib for easy deployment

fangq · Aug 4, 2023 · 97fff3e · 97fff3e
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commit 97fff3e
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diff --git a/.github/workflows/build_all.yml b/.github/workflows/build_all.yml
@@ -88,18 +88,6 @@ jobs:
           cuda: '9.2.148'
           method: 'network'
           sub-packages: '["nvcc"]'
-      - name: Install Zlib Dev (Windows Only)
-        if: ${{ runner.os == 'Windows' }}
-        run: |
-          curl.exe --retry 3 -kL https://www.bruot.org/hp/media/files/libraries/zlib_1_2_11_msvc2017_64.zip --output zlib.zip
-          unzip zlib.zip -d zlib
-          mv zlib/msvc2017_64/* zlib/
-          mv zlib/include/zlib/* zlib/include
-          mv zlib/lib/zlib/* zlib/lib
-          perl -pi -e 's/#if 1\s+.*HAVE_UNISTD_H.*/#if 0/g' zlib/include/zconf.h
-          echo "CMAKE_INCLUDE_PATH=$PWD\zlib\include" >> $GITHUB_ENV
-          echo "CMAKE_LIBRARY_PATH=$PWD\zlib\lib" >> $GITHUB_ENV
-          rm zlib.zip
       - name: Link libgomp.a (MacOS only)
         if: ${{ runner.os == 'macOS' }}
         run: |
@@ -138,7 +126,7 @@ jobs:
         run: |
           cd src
           if [[ "$RUNNER_OS" == "Windows" ]]; then
-            make mex INCLUDES='-I"${{ env.CMAKE_INCLUDE_PATH }}"' LIBRARIES='../zlib/lib/zlibstatic.lib'
+            make mex INCLUDES='-I"${{ env.CMAKE_INCLUDE_PATH }}"'
             objdump -p ../mcxlab/mcx.mexw* | grep "DLL Name:"
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
             which mex
@@ -155,13 +143,13 @@ jobs:
           cd src
           make clean
           if [[ "$RUNNER_OS" == "Linux" ]]; then
-            make AR=g++ BACKEND=cudastatic USERLINKOPT='libzmat.a -Wl,-Bstatic -lgomp -lz -Wl,-Bdynamic'
+            make AR=g++ BACKEND=cudastatic USERLINKOPT='libzmat.a -Wl,-Bstatic -lgomp -Wl,-Bdynamic'
             ldd ../bin/mcx
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
             make BACKEND=cudastatic CC=gcc-10 CXX=g++-10
             otool -L ../bin/mcx
           else
-            make static INCLUDES='-I"${{ env.CMAKE_INCLUDE_PATH }}"' LIBRARIES='../zlib/lib/zlibstatic.lib' ZLIBFLAG=''
+            make static INCLUDES='-I"${{ env.CMAKE_INCLUDE_PATH }}"'
             #objdump -p ../bin/mcx | grep "DLL Name:"
           fi
       - name: Build mcxstudio
@@ -203,7 +191,7 @@ jobs:
             cp -a src/mcstudio/mcxshow.app   bin
             cp -a src/mcstudio/mcxviewer.app bin
           elif [[ "$RUNNER_OS" == "Windows" ]]; then
-            rm -rf octave zlib cuda_installer* bin/mcx.lib bin/mcx.exp
+            rm -rf octave cuda_installer* bin/mcx.lib bin/mcx.exp
             strip -S bin/*
             upx/upx-4.0.2-win64/upx -9 bin/*
             rm -rf upx

diff --git a/.github/workflows/build_windows_wheel.yml b/.github/workflows/build_windows_wheel.yml
@@ -46,13 +46,6 @@ jobs:
           $CUDA_PATH=Get-ChildItem "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA" -filter "v*.*" -Directory | % { $_.fullname }
           echo "CUDA_PATH=$CUDA_PATH" >> $env:GITHUB_ENV
           echo "CUDA_TOOLKIT_ROOT_DIR=$CUDA_PATH" >> $env:GITHUB_ENV
-      - name: Install Zlib Dev
-        run: |
-          curl.exe --retry 3 -kL https://cytranet.dl.sourceforge.net/project/gnuwin32/zlib/1.2.3/zlib-1.2.3-lib.zip --output zlib.zip
-          Expand-Archive .\zlib.zip -DestinationPath zlib\
-          echo "CMAKE_INCLUDE_PATH=$PWD\zlib\include" >> $env:GITHUB_ENV
-          echo "CMAKE_LIBRARY_PATH=$PWD\zlib\lib" >> $env:GITHUB_ENV
-          rm zlib.zip
       - name: Build Wheels
         run: |
           cd pmcx/

diff --git a/pmcx/README.md b/pmcx/README.md
@@ -5,7 +5,7 @@
 - Copyright: (C) Matin Raayai Ardakani (2022-2023) <raayaiardakani.m at northeastern.edu> 
 and Qianqian Fang (2019-2023) <q.fang at neu.edu>
 - License: GNU Public License V3 or later
-- Version: 0.0.14
+- Version: 0.0.15
 - URL: https://pypi.org/project/pmcx/
 - Github: https://github.com/fangq/mcx
 
@@ -87,16 +87,6 @@ The NVIDIA GPU driver of the target system must support the selected CUDA toolki
   CMake is also widely available on package managers across all operating systems.
   Additionally, on Windows, make sure **Visual Studio's C++ CMake tools for Windows** is also installed by selecting its option
   during installation.
-* **Zlib Compression Development Headers**: On Linux, this is generally available via the built-in package manager. For 
-  example, on Debian-based distributions like Ubuntu it is available via ```apt``` under the name ```zlib1g-dev```. On
-  macOS, brew provides it under the name ```zlib```. No packaged versions of Zlib are available for windows, therefore it must be
-  downloaded manually and added to the CMake environment variables in your working Powershell session:
-  ```powershell
-    curl.exe --retry 3 -kL https://cytranet.dl.sourceforge.net/project/gnuwin32/zlib/1.2.3/zlib-1.2.3-lib.zip --output zlib.zip
-    Expand-Archive .\zlib.zip -DestinationPath zlib\
-    $env:CMAKE_INCLUDE_PATH=$PWD\zlib\include
-    $env:CMAKE_LIBRARY_PATH=$PWD\zlib\lib
-  ```
 
 ### Build Steps
 1. Ensure that ```cmake```, ```nvcc``` (NVIDIA CUDA Compiler) and the C/C++ compiler are all located over your ```PATH```.

diff --git a/pmcx/pmcx/__init__.py b/pmcx/pmcx/__init__.py
@@ -38,6 +38,6 @@
 # from .files import loadmc2, loadmch, load, save
 from .bench import bench
 
-__version__ = "0.0.14"
+__version__ = "0.0.15"
 
 __all__ = ("gpuinfo", "run", "bench", "detweight", "cwdref")
diff --git a/pmcx/setup.py b/pmcx/setup.py
@@ -119,7 +119,7 @@ def build_extension(self, ext):
 setup(
     name="pmcx",
     packages=['pmcx'],
-    version="0.0.14",
+    version="0.0.15",
     requires=['numpy'],
     license='GPLv3+',
     author="Matin Raayai Ardakani, Qianqian Fang",

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -15,7 +15,6 @@ cmake_minimum_required(VERSION 3.3)
 
 project(mcx)
 
-find_package(ZLIB REQUIRED)
 find_package(CUDA QUIET REQUIRED)
 
 find_package(OpenMP REQUIRED)
@@ -50,6 +49,7 @@ set(
 set(CMAKE_C_FLAGS "-g -Wall -std=c99 -fPIC")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../lib)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # Add include directories
 include_directories(cjson ubj zmat zmat/easylzma)
@@ -91,7 +91,6 @@ target_link_libraries(
     mcx-exe
     mcx OpenMP::OpenMP_CXX
     zmat
-    ZLIB::ZLIB
     )
 
 if (BUILD_PYTHON)

diff --git a/src/Makefile b/src/Makefile
@@ -29,8 +29,8 @@ OUTPUT_DIR=$(MCXDIR)/bin
 DOXY       := doxygen
 DOCDIR     := $(MCXDIR)/doc
 DOXYCFG=mcx_doxygen.cfg
-ZMATLIB    :=libzmat.a
-ZLIBFLAG   :=-lz
+ZMATLIB    :=lib/libzmat.a
+ZLIBFLAG   :=
 USERLINKOPT?=$(ZMATLIB) $(ZLIBFLAG)
 
 CUDART=-lcudart
@@ -94,7 +94,7 @@ ifeq ($(findstring _NT-,$(PLATFORM)), _NT-)
   CPPFLAGS=-g
   CUDA_STATIC=--cudart static $(NVCCOMP) -Xcompiler "-MT"
   CPPOPT+=$(NVCCOMP)
-  ZLIBFLAG?=-lzlib
+  ZLIBFLAG?=
   ZMATLIB    :=zmat/zmatlib.obj zmat/lz4/lz4.obj zmat/lz4/lz4hc.obj zmat/easylzma/*.obj zmat/easylzma/pavlov/*.obj
   USERLINKOPT:=${LIBRARIES} $(ZMATLIB) $(ZLIBFLAG)
 else ifeq ($(findstring Darwin,$(PLATFORM)), Darwin)

diff --git a/src/zmat/CMakeLists.txt b/src/zmat/CMakeLists.txt
@@ -14,12 +14,13 @@ find_package(ZLIB REQUIRED)
 option(STATIC_LIB "Build static library" ON)
 
 # C Options
-set(CMAKE_C_FLAGS "-g -Wall -O3 -fPIC")
+set(CMAKE_C_FLAGS "-g -Wall -O3 -fPIC -DNO_BLOSC2 -DNO_ZLIB -DNO_ZSTD -D_LARGEFILE64_SOURCE=1")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../)
 
 # Add include directories
 #include_directories(./)
 include_directories(lz4)
+include_directories(miniz)
 include_directories(easylzma)
 include_directories(easylzma/pavlov)
 
@@ -30,6 +31,8 @@ if(STATIC_LIB)
     zmatlib.c
     lz4/lz4.c
     lz4/lz4hc.c
+    miniz/miniz.c
+    miniz/miniz.h
     easylzma/compress.c
     easylzma/decompress.c
     easylzma/lzma_header.c
@@ -50,6 +53,8 @@ else()
     zmatlib.c
     lz4/lz4.c
     lz4/lz4hc.c
+    miniz/miniz.c
+    miniz/miniz.h
     easylzma/compress.c
     easylzma/decompress.c
     easylzma/lzma_header.c