Add support for mesa>11035

This has moved all the shared library building logic into mesa itself
thus now we just need to flip an option in the makefile and recompile

README.md

@@ -13,16 +13,16 @@ Note: pyMesa currently only works on linux, macs will fail to build.
 
 [gfort2py](https://github.com/rjfarmer/gfort2py) (Also available via pip) (needs version >= 1.0.11)
 
-numpy
+All versions need numpy and patch
+
+if using MESA <  11035 then you also need:
 
 libtool
 
 automake
 
 chrpath
-
-patch 
-
+
 ## Building
 
 ### SDK's
@@ -42,6 +42,9 @@ chmod u+x mesa-setup.sh
 
 This script should only be run once to setup up mesa. It can be ran again if you do a ./clean inside the MESA_DIR.
 
+#### MESA < 11035
+If using mesa version < 11035 then the following applies:
+
 Adipls, gyre and stella are not currently built as part of this.
 
 While we can use the individual MESA modules we can not currently run a full star (or binary) model, in either python or fortran.
@@ -51,6 +54,7 @@ While we can use the individual MESA modules we can not currently run a full sta
 - 10000
 - 10108
 - 10398
+- >11035 (non released mesa version)
 
 Other versions can be supported upon request.
 
@@ -66,14 +70,15 @@ Will override the version check and attempt to build MESA using the patches for
 ````bash
 # Set MESA_DIR and initialize the sdk
 
+# If using MESA < 11035 set the LD_LIBRARY_PATH
 export LD_LIBRARY_PATH=$MESA_DIR/lib:$LD_LIBRARY_PATH
 python3
 ````
 
 ## Structure
 
 The only python file that is actually needed to run this is pyMesaUtils.py. This file contains the code needed to interface with mesa. Inside the mesa_models/ folder
-contain examples of how to interface with most of meas's modules. pydfriddr/ folder contains examples for testing MESA's analytic derivatives with a numerical derivative.
+contain examples of how to interface with most of MESA's modules. pydfriddr/ folder contains examples for testing MESA's analytic derivatives with a numerical derivative.
 
 
 ## Usage
@@ -157,6 +162,8 @@ An example of this can be found in eos.py.
 
 ## Uninstalling
 
+If using MESA < 11035:
+
 The best bet is just to re-download mesa, during the setup phase we alter a lot of files. If you want to try to keep your MESA_DIR then something like this should work:
 
 ````bash
@@ -176,6 +183,9 @@ rm -rf $MESA_DIR/crlibm/crlibm-patches $MESA_DIR/{star,binary}/skip_test
 
 ````
 
+If using MESA >= 11035, then in utils/makefile_header switch USE_SHARED=YES to USE_SHARED=NO and do a ./clean
+and ./mk in $MESA_DIR
+
 
 ## Bug reports:
 
@@ -191,7 +201,7 @@ or issues on the github tracker.
 
 ## Citating
 
-People who use pyMESA in papers should cite this using the zenodo link for the version they used. If you use pyMesa in a project (resaech or teaching), let me know and i can help advertise here (also useful for me to help
+People who use pyMESA in papers should cite this using the zenodo link for the version they used. If you use pyMesa in a project (research or teaching), let me know and i can help advertise here (also useful for me to help
 with funding requests). Current versions citation is in the CITATION file.
 
 ## Known Projects using pyMesa

mesa-setup.sh

@@ -34,6 +34,8 @@ if [[ ! "$PATH" == *"$MESASDK_ROOT"* ]];then
     exit 1
 fi
 
+DO_NOTHING=0
+
 MESA_VERSION=$(<"$MESA_DIR/data/version_number")
 
 export SHARED_LIB=so
@@ -101,7 +103,9 @@ then
     #if [[ "$SDK_HAS_LAPACK_SO" == "1" ]]; then
         #cp patches/0003-sdk-with-lapack-10000.patch "$MESA_DIR"/patches/.
     #fi
-
+elif [[ "$MESA_VERSION" -gt 11035 ]]
+then
+    cp patches/0001-turn-shared-on.patch "$MESA_DIR"/patches/.
 else
     echo "MESA version $MESA_VERSION is not supported"
     echo "Open an issue on github to request your mesa version"
@@ -118,16 +122,22 @@ cd "$MESA_DIR"
 echo "Clean MESA"
 ./clean
 
-#Skip Tests in star as we can't run a full model yet
-/usr/bin/touch star/skip_test
-/usr/bin/touch binary/skip_test
+if [[ "$MESA_VERSION" -lt 11035 ]]
+then
+    #Skip Tests in star as we can't run a full model yet
+    /usr/bin/touch star/skip_test
+    /usr/bin/touch binary/skip_test
+fi
 
 if [ -z "$PYMESA_SKIP_PATCH" ]
 then
 	echo "Patching mesa"
 
-	mkdir -p "$MESA_DIR/crlibm/crlibm-patches"
-
+    if [[ "$MESA_VERSION" -lt 11035 ]]
+    then
+        mkdir -p "$MESA_DIR/crlibm/crlibm-patches"
+	fi
+
 	for i in patches/*;
 	do
 	    patch -f -p1 < $i
@@ -141,12 +151,16 @@ then
     exit 0
 fi
 
-if [[ "$(uname)" == "Darwin" ]];then
-    export DYLD_LIBRARY_PATH=../../make:../make:$MESA_DIR/lib:$DYLD_LIBRARY_PATH
-else
-    export LD_LIBRARY_PATH=../../make:../make:$MESA_DIR/lib:$LD_LIBRARY_PATH
+if [[ "$MESA_VERSION" -lt 11035 ]]
+then
+    if [[ "$(uname)" == "Darwin" ]];then
+        export DYLD_LIBRARY_PATH=../../make:../make:$MESA_DIR/lib:$DYLD_LIBRARY_PATH
+    else
+        export LD_LIBRARY_PATH=../../make:../make:$MESA_DIR/lib:$LD_LIBRARY_PATH
+    fi
 fi
 
+
 ./mk
 if [[ $? != 0 ]] || [[ ! -f "$MESA_DIR/lib/libstar.$SHARED_LIB" ]]  ;then
     echo
@@ -161,24 +175,39 @@ if [[ $? != 0 ]] || [[ ! -f "$MESA_DIR/lib/libstar.$SHARED_LIB" ]]  ;then
     exit 1
 fi
 
-echo
-echo
-echo
-echo "****************************************************************"
-echo "pyMESA build was succesfull"
-if [[ "$(uname)" == "Darwin" ]];then
-    echo "Each time you wish to use this you must set the DYLD_LIBRARAY_PATH variable"
-else
-    echo "Each time you wish to use this you must set the LD_LIBRARAY_PATH variable"
-fi
-echo "After the mesasdk has been initilized:"
-if [[ "$(uname)" == "Darwin" ]];then
-    echo 'export DYLD_LIBRARY_PATH=$MESA_DIR/lib:$DYLD_LIBRARY_PATH'
+if [[ "$MESA_VERSION" -lt 11035 ]]
+then
+    echo
+    echo
+    echo
+    echo "****************************************************************"
+    echo "pyMESA build was succesfull"
+    if [[ "$(uname)" == "Darwin" ]];then
+        echo "Each time you wish to use this you must set the DYLD_LIBRARAY_PATH variable"
+    else
+        echo "Each time you wish to use this you must set the LD_LIBRARAY_PATH variable"
+    fi
+    echo "After the mesasdk has been initilized:"
+    if [[ "$(uname)" == "Darwin" ]];then
+        echo 'export DYLD_LIBRARY_PATH=$MESA_DIR/lib:$DYLD_LIBRARY_PATH'
+    else
+        echo 'export LD_LIBRARY_PATH=$MESA_DIR/lib:$LD_LIBRARY_PATH'
+    fi
+    echo "Do not run this script again on the same MESA_DIR"
+    echo "****************************************************************"
+    echo
+    echo
+    echo
 else
-    echo 'export LD_LIBRARY_PATH=$MESA_DIR/lib:$LD_LIBRARY_PATH'
+    echo
+    echo
+    echo
+    echo "****************************************************************"
+    echo "pyMESA build was succesfull"
+    echo "****************************************************************"
+    echo
+    echo
+    echo
+
 fi
-echo "Do not run this script again on the same MESA_DIR"
-echo "****************************************************************"
-echo
-echo
-echo
+

patches/0001-turn-shared-on.patch

@@ -0,0 +1,25 @@
+From 0d8d4c40c318afcddd18a99ebd82edc7c036a69b Mon Sep 17 00:00:00 2001
+From: Robert Farmer <[email protected]>
+Date: Fri, 7 Sep 2018 15:04:04 +0200
+Subject: [PATCH] turn shared on
+
+---
+ utils/makefile_header | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/utils/makefile_header b/utils/makefile_header
+index c22aa247f..688b4cf2f 100644
+--- a/utils/makefile_header
++++ b/utils/makefile_header
+@@ -86,7 +86,7 @@ USE_STUB_FOR_CRLIBM = NO
+
+ # step 9) Build shared libraries? Needed if you want mesa to be usable in python
+
+-USE_SHARED = NO
++USE_SHARED = YES
+
+
+ #################################################################
+-- 
+2.17.1
+

pyMesaUtils.py

@@ -51,12 +51,6 @@ def _versiontuple(v):
 LIB_DIR = os.path.join(MESA_DIR,'lib')
 INCLUDE_DIR = os.path.join(MESA_DIR,'include')
 
-if "LD_LIBRARY_PATH" not in os.environ:
-    raise ValueError("Must set LD_LIBRARY_PATH environment variable")
-elif LIB_DIR not in os.environ['LD_LIBRARY_PATH']:
-    raise ValueError("Must have $MESA_DIR/lib in LD_LIBRARY_PATH environment variable")
-
-
 RATES_DATA=os.path.join(DATA_DIR,'rates_data')
 EOSDT_DATA=os.path.join(DATA_DIR,'eosDT_data')
 EOSPT_DATA=os.path.join(DATA_DIR,'eosPT_data')
@@ -78,6 +72,12 @@ def _versiontuple(v):
     v=f.readline().strip()
     MESA_VERSION=int(v)
 
+if MESA_VERSION < 11035:
+    if "LD_LIBRARY_PATH" not in os.environ:
+        raise ValueError("Must set LD_LIBRARY_PATH environment variable")
+    elif LIB_DIR not in os.environ['LD_LIBRARY_PATH']:
+        raise ValueError("Must have $MESA_DIR/lib in LD_LIBRARY_PATH environment variable")
+
 p=sys.platform.lower()
 
 if p == "linux" or p == "linux2":
@@ -135,23 +135,37 @@ def buildModule(module):
     finally:
         os.chdir(cwd)
 
-    os.chdir(LIB_DIR)
-    try:
-        x = subprocess.call("chrpath -r lib"+module+"."+LIB_EXT,shell=True)
-        if x:
-            raise ValueError("chrpath failed")
-    except:
-        raise
-    finally:
-        os.chdir(cwd)
+    if MESA_VERSION < 11035:
+        os.chdir(LIB_DIR)
+        try:
+            x = subprocess.call("chrpath -r lib"+module+"."+LIB_EXT,shell=True)
+            if x:
+                raise ValueError("chrpath failed")
+        except:
+            raise
+        finally:
+            os.chdir(cwd)
 
     print("Built "+str(module))
 
 def buildRunStarSupport():
     cwd = os.getcwd()
     os.chdir(os.path.join(MESA_DIR,'star','make'))
     try:
-        x = subprocess.call('gfortran -Wno-uninitialized -fno-range-check -fmax-errors=12 -fPIC -shared -fprotect-parens -fno-sign-zero -fbacktrace -ggdb -finit-real=snan -fopenmp  -std=f2008 -Wno-error=tabs -I../public -I../private -I../../include -I'+os.path.join(MESASDK_ROOT,'include')+' -Wunused-value -Werror -W -Wno-compare-reals -Wno-unused-parameter -fimplicit-none  -O2 -ffree-form -x f95-cpp-input -I../defaults -I../job -I../other ../job/run_star_support.f90 -o librun_star_support.'+SHARED_LIB,shell=True)
+        compile_cmd = ['gfortran -Wno-uninitialized -fno-range-check',
+                      '-fmax-errors=12 -fPIC -shared -fprotect-parens',
+                      '-fno-sign-zero -fbacktrace -ggdb -finit-real=snan',
+                      '-fopenmp  -std=f2008 -Wno-error=tabs -I../public',
+                      '-I../private -I../../include',
+                      '-I'+os.path.join(MESASDK_ROOT,'include'),
+                      '-Wunused-value -Werror -W -Wno-compare-reals',
+                      '-Wno-unused-parameter -fimplicit-none  -O2',
+                      '-ffree-form -x f95-cpp-input -I../defaults',
+                      '-I../job -I../other ../job/run_star_support.f90',
+                      '-Wl,-rpath=' + LIB_DIR,
+                      '-o librun_star_support.'+LIB_EXT]
+
+        x = subprocess.call(" ".join(compile_cmd),shell=True))
         if x:
             raise ValueError("Build run_star_support failed")
     except: