Conda package for cpptraj

Makefile

@@ -33,8 +33,8 @@ unittest: config.h
 # Clean up
 clean: config.h
 	cd src && $(MAKE) clean
-	cd test && $(MAKE) clean
-	cd unitTests && $(MAKE) clean
+#	cd test && $(MAKE) clean
+#	cd unitTests && $(MAKE) clean
 
 docs: src/cpptraj.Doxyfile
 	cd doc && make docs

configure

@@ -1073,7 +1073,7 @@ EOF
 TestReadline() {
   cat > testp.cpp <<EOF
 #include <cstdio>
-#include <readline.h>
+#include <readline/readline.h>
 static char *line_read = (char *)NULL;
 // Do not want to actually run this so leave outside main
 void Unused() { line_read = readline(""); }
@@ -1514,11 +1514,11 @@ SetupLibraries() {
         if [ $i -eq $LREADLINE ] ; then
           # For external readline, we need to link libtermcap for windows
           # and libncurses for Linux
-          #if [ $USE_WINDOWS -eq 1 ]; then
+          if [ $USE_WINDOWS -eq 1 ]; then
             lflag="$lflag -ltermcap"
-          #else
-          #  lflag="$lflag -lncurses"
-          #fi
+          else
+            lflag="$lflag -lncurses"
+          fi
         elif [ $i -eq $LSANDER ] ; then
           # Always specify libsander location to prevent pulling in
           # other amber libraries.
@@ -1662,7 +1662,7 @@ SetupCompilers() {
       if [ -z "$FC" ]; then FC=gfortran; fi
       hostflags=''
       optflags='-O3'
-      ompflag='-fopenmp'
+      ompflag='-Xclang -fopenmp'
       freefmtflag='-ffree-form'
       foptflags='-O3'
       FLINK='-lgfortran'

mkrelease

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+version=$1
+
+tar cvf ../cpptraj-$version.tar configure dat get_library.sh \
+   LICENSE Makefile src test doc README.md
+cd ..
+gzip cpptraj-$version.tar
+
+rsync -av cpptraj-$version.tar.gz \
+    [email protected]:ambermd-website.rcsb.rutgers.edu/downloads
+
+curl -sL https://ambermd.org/downloads/cpptraj-$version.tar.gz | openssl sha256
+

recipe/activate.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+export CPPTRAJHOME=${CONDA_PREFIX}
+

recipe/build.sh

@@ -0,0 +1,41 @@
+#!/bin/sh
+
+export NVCC=nvcc
+# export SHADER_MODEL=sm_89
+
+arch=`uname`
+
+if [ "$arch" == "Darwin" ]; then
+
+   ./configure  -openmp -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang
+   make install
+   make clean
+   ./configure -mpi -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang
+   make install
+   make clean
+   ./configure -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang
+   make install
+
+else
+
+   ./configure -cuda -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu
+   make install
+   make clean
+   ./configure -mpi -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu
+   make install
+   make clean
+   ./configure  -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu
+   make install
+
+fi
+
+
+rsync -a README.md config.h LICENSE dat bin lib test $PREFIX
+
+mkdir -p $PREFIX/doc
+rsync -a doc/CpptrajManual.pdf $PREFIX/doc
+
+# Export CPPTRAJHOME automatically
+mkdir -p ${PREFIX}/etc/conda/{activate,deactivate}.d
+cp ${RECIPE_DIR}/activate.sh ${PREFIX}/etc/conda/activate.d/cpptraj.sh
+cp ${RECIPE_DIR}/deactivate.sh ${PREFIX}/etc/conda/deactivate.d/cpptraj.sh

recipe/conda_build_config.yaml

@@ -0,0 +1,8 @@
+c_compiler_version:
+  - 11.4.0 # [linux]
+
+cxx_compiler_version:
+  - 11.4.0 # [linux]
+
+fortran_compiler_version:
+  - 11.4.0 # [linux]

recipe/deactivate.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+unset CPPTRAJHOME
+

recipe/meta.yaml

@@ -0,0 +1,84 @@
+{% set version = "0.4" %}
+{% set mpi = "mpich" %}
+
+package:
+  name: cpptraj
+#  version 0.1   trying to adapt recipe from AmberClassic
+#  version 0.2   small tweaks get allow osx-64 build
+#  version 0.3   add mpi and pnetcdf support
+#  version 0.4   build from url; add cuda
+  version: {{ version }}
+
+source:
+  path: ../
+# url: https://ambermd.org/downloads/cpptraj-{{ version }}.tar.gz
+# sha256: 6be4dda3f6f59610d97b2cdb8f6745ca05cff60705ba95dbcfc07c10fd083d95
+
+build:
+  number: 1
+  skip: True # [win or ppc65le or aarch64]
+
+mpi:
+   - {{ mpi }}
+
+requirements:
+  build:
+   - make
+   - {{ compiler('fortran') }}
+   - {{ compiler('c') }}
+   - {{ compiler('cxx') }}
+   - {{ mpi }} # [ mpi == "mpich" ]
+   - libpnetcdf
+   - {{ compiler('nvcc') }} # [ linux ]
+   - coreutils # [ linux ]
+   - nvcc_linux-64 # [ linux ]
+   - llvm-openmp  # [osx]
+   - libgomp      # [linux]
+   - fftw
+   - readline
+   - libnetcdf
+   - netcdf-fortran
+
+  host:
+   - openblas
+   - arpack
+   - openmm
+   - libnetcdf
+   - netcdf-fortran
+   - llvm-openmp  # [osx]
+   - libgomp      # [linux and not aarch64]
+   - {{ mpi }} # [ mpi == "mpich" ]
+   - libpnetcdf
+   - fftw
+   - readline
+
+  run:
+   - llvm-openmp  # [osx]
+   - libgomp      # [linux and not aarch64]
+   - openblas
+   - arpack
+   - openmm
+   - libnetcdf
+   - netcdf-fortran
+   - {{ mpi }} # [ mpi == "mpich" ]
+   - libpnetcdf
+   - fftw
+   - readline
+
+test:
+  commands:
+   - cpptraj --help
+
+about:
+    home: https://github.com/Amber-MD/cpptraj.git
+    license: GPL-3.0-or-later
+    license_file: 
+       - LICENSE
+    summary: 'Performs analysis of MD trajectories, especially for biomolecules'
+    description: |
+      CPPTRAJ is a program designed to process and analyze molecular
+      dynamics trajectories and relevant data sets derived from their
+      analysis. CPPTRAJ supports many popular MD software packages including
+      Amber, CHARMM, Gromacs, and NAMD.
+
+

src/Matrix.h

@@ -2,6 +2,7 @@
 #define INC_MATRIX_H
 #include "ArrayIterator.h"
 #include <cmath> // For linear least squares
+#include <algorithm> // For copy()
 /// Two-dimensional matrix template.
 template <class T> class Matrix {
 // TODO: Type may not be necessary here if in DataSet_2D

src/ReadLine.cpp

@@ -8,8 +8,8 @@
 #   include <iostream>
 #else
 #   define READLINE_LIBRARY
-#   include <readline.h>
-#   include <history.h>
+#   include <readline/readline.h>
+#   include <readline/history.h>
 #endif
 #include "ReadLine.h"
 #include "Command.h"