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ufz / iphreeqc

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[SOLVED] Build successful on Android arm64 but loading fails #3

Closed defencedog closed 11 months ago

defencedog commented 11 months ago

Build log. Incorporated only first patch from https://github.com/ufz/iphreeqc/issues/2#issuecomment-867954005

Making all in src
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
  CXX      IPhreeqc.lo
  CXX      phreeqcpp/cvode.lo
  CXX      phreeqcpp/advection.lo
  CXX      phreeqcpp/cxxKinetics.lo
  CXX      phreeqcpp/basicsubs.lo
  CXX      phreeqcpp/cl1.lo
  CXX      phreeqcpp/cxxMix.lo
  CXX      phreeqcpp/cvdense.lo
  CXX      phreeqcpp/Exchange.lo
  CXX      phreeqcpp/ExchComp.lo
  CXX      phreeqcpp/GasComp.lo
  CXX      phreeqcpp/gases.lo
  CXX      phreeqcpp/GasPhase.lo
  CXX      phreeqcpp/input.lo
  CXX      phreeqcpp/integrate.lo
  CXX      phreeqcpp/inverse.lo
  CXX      phreeqcpp/ISolution.lo
  CXX      phreeqcpp/isotopes.lo
  CXX      phreeqcpp/kinetics.lo
  CXX      phreeqcpp/KineticsComp.lo
  CXX      phreeqcpp/mainsubs.lo
  CXX      phreeqcpp/model.lo
phreeqcpp/inverse.cpp:5109:9: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
                if (c != EOF && c != '\n' && i != MAX_LINE)
                    ~ ^  ~~~
phreeqcpp/inverse.cpp:5133:9: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                if (c == EOF)
                    ~ ^  ~~~
2 warnings generated.
  CXX      phreeqcpp/NameDouble.lo
  CXX      phreeqcpp/nvector.lo
  CXX      phreeqcpp/nvector_serial.lo
  CXX      phreeqcpp/parse.lo
  CXX      phreeqcpp/PBasic.lo
  CXX      phreeqcpp/phqalloc.lo
  CXX      phreeqcpp/Phreeqc.lo
  CXX      phreeqcpp/PHRQ_io_output.lo
  CXX      phreeqcpp/pitzer.lo
  CXX      phreeqcpp/pitzer_structures.lo
  CXX      phreeqcpp/PPassemblage.lo
  CXX      phreeqcpp/PPassemblageComp.lo
  CXX      phreeqcpp/prep.lo
  CXX      phreeqcpp/Pressure.lo
  CXX      phreeqcpp/print.lo
  CXX      phreeqcpp/Reaction.lo
  CXX      phreeqcpp/read.lo
phreeqcpp/print.cpp:1461:67: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                           "Molality", "Activity", "Molality", "Activity", "Gamma", "cm<B3>/mol"));
                                                                                       ^~~~
phreeqcpp/print.cpp:1629:46: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                output_msg(sformatf("\t%11.3e  sigma, C/m<B2>\n",
                                                                         ^~~~
phreeqcpp/print.cpp:1640:49: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                output_msg(sformatf("\tundefined  sigma, C/m<B2>\n"));
                                                                            ^~~~
phreeqcpp/print.cpp:1662:37: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  specific area, m<B2>/mol %s\n",
                                                                              ^~~~
phreeqcpp/print.cpp:1670:22: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  m<B2> for %11.3e moles of %s\n\n",
                                                               ^~~~
phreeqcpp/print.cpp:1683:37: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  specific area, m<B2>/mol %s\n",
                                                                              ^~~~
phreeqcpp/print.cpp:1691:22: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  m<B2> for %11.3e moles of %s\n\n",
                                                               ^~~~
phreeqcpp/print.cpp:1704:37: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  specific area, m<B2>/g\n",
                                                                              ^~~~
phreeqcpp/print.cpp:1710:37: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                output_msg(sformatf("\t%11.3e  m<B2> for %11.3e g\n\n",
                                                                ^~~~
phreeqcpp/print.cpp:1925:40: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  sigma, plane 0, C/m<B2>\n",
                                                                                 ^~~~
phreeqcpp/print.cpp:1932:40: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  sigma, plane 1, C/m<B2>\n",
                                                                                 ^~~~
phreeqcpp/print.cpp:1939:40: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  sigma, plane 2, C/m<B2>\n",
                                                                                 ^~~~
phreeqcpp/print.cpp:1946:46: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                                   "\t%11.3e  sigma, diffuse layer, C/m<B2>\n\n",
                                                                                       ^~~~
phreeqcpp/print.cpp:1955:49: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                output_msg(sformatf("\tundefined  sigma, C/m<B2>\n"));
                                                                            ^~~~
phreeqcpp/print.cpp:2214:31: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                   "Specific Conductance (<B5>S/cm, ", tc_x, "<B0>C)  = ", (int) SC));
                                                          ^~~~
phreeqcpp/print.cpp:2214:48: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                                   "Specific Conductance (<B5>S/cm, ", tc_x, "<B0>C)  = ", (int) SC));
                                                                              ^~~~
phreeqcpp/print.cpp:2224:50: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
                output_msg(sformatf("%45s%9.5f", "Density (g/cm<B3>)  = ",
                                                               ^~~~
phreeqcpp/print.cpp:2279:51: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
        output_msg(sformatf("%45s%6.2f\n", "Temperature (<B0>C)  = ",
                                                         ^~~~
  CXX      phreeqcpp/ReadClass.lo
18 warnings generated.
  CXX      phreeqcpp/readtr.lo
  CXX      phreeqcpp/runner.lo
  CXX      phreeqcpp/SelectedOutput.lo
  CXX      phreeqcpp/Serializer.lo
  CXX      phreeqcpp/sit.lo
  CXX      phreeqcpp/smalldense.lo
  CXX      phreeqcpp/Solution.lo
  CXX      phreeqcpp/SolutionIsotope.lo
  CXX      phreeqcpp/spread.lo
  CXX      phreeqcpp/SS.lo
  CXX      phreeqcpp/SSassemblage.lo
  CXX      phreeqcpp/SScomp.lo
  CXX      phreeqcpp/step.lo
  CXX      phreeqcpp/StorageBin.lo
  CXX      phreeqcpp/StorageBinList.lo
  CXX      phreeqcpp/structures.lo
  CXX      phreeqcpp/sundialsmath.lo
  CXX      phreeqcpp/Surface.lo
  CXX      phreeqcpp/SurfaceCharge.lo
  CXX      phreeqcpp/SurfaceComp.lo
  CXX      phreeqcpp/System.lo
  CXX      phreeqcpp/tally.lo
  CXX      phreeqcpp/Temperature.lo
  CXX      phreeqcpp/tidy.lo
  CXX      phreeqcpp/transport.lo
  CXX      phreeqcpp/Use.lo
  CXX      phreeqcpp/UserPunch.lo
  CXX      phreeqcpp/utilities.lo
  CC       Var.lo
  CXX      phreeqcpp/PhreeqcKeywords/Keywords.lo
  CXXLD    libiphreeqc.la
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
Making all in tests
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
Making all in examples
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
Making all in doc
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
Making all in database
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
Making all in gtest
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'

Install log

~/iphreeqc-3.7.3-15968 $ make install
Making install in src
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/lib'
 /bin/sh ../libtool   --mode=install /data/data/com.termux/files/usr/bin/install -c   libiphreeqc.la '/data/data/com.termux/files/usr/local/lib'
libtool: install: /data/data/com.termux/files/usr/bin/install -c .libs/libiphreeqc-3.7.3.so /data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so
libtool: install: (cd /data/data/com.termux/files/usr/local/lib && { ln -s -f libiphreeqc-3.7.3.so libiphreeqc.so || { rm -f libiphreeqc.so && ln -s libiphreeqc-3.7.3.so libiphreeqc.so; }; })
libtool: install: /data/data/com.termux/files/usr/bin/install -c .libs/libiphreeqc.lai /data/data/com.termux/files/usr/local/lib/libiphreeqc.la
libtool: install: /data/data/com.termux/files/usr/bin/install -c .libs/libiphreeqc.a /data/data/com.termux/files/usr/local/lib/libiphreeqc.a
libtool: install: chmod 644 /data/data/com.termux/files/usr/local/lib/libiphreeqc.a
libtool: install: ranlib /data/data/com.termux/files/usr/local/lib/libiphreeqc.a
libtool: finish: PATH="/data/data/com.termux/files/usr/bin:/data/data/com.termux/files/usr/bin:/data/data/com.termux/files/usr/local/bin:/sbin" ldconfig -n /data/data/com.termux/files/usr/local/lib
/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/libtool: 1: eval: ldconfig: not found
----------------------------------------------------------------------
Libraries have been installed in:
   /data/data/com.termux/files/usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator run these commands:

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/src'
 /data/data/com.termux/files/usr/bin/install -c -m 644 ../src/README.Fortran ../src/IPhreeqc_interface.F90 '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/src'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/include'
 /data/data/com.termux/files/usr/bin/install -c -m 644 ../src/IPhreeqc.h ../src/IPhreeqc.hpp ../src/IPhreeqcCallbacks.h ../src/Var.h ../src/phreeqcpp/common/PHRQ_io.h ../src/phreeqcpp/PhreeqcKeywords/Keywords.h '/data/data/com.termux/files/usr/local/include'
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/src'
Making install in tests
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/tests'
Making install in examples
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
make[2]: Nothing to be done for 'install-exec-am'.
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/c/advect'
 /data/data/com.termux/files/usr/bin/install -c -m 644 c/advect/advect.c c/advect/ic c/advect/phreeqc.dat '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/c/advect'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/com/excel'
 /data/data/com.termux/files/usr/bin/install -c -m 644 com/excel/phreeqc.dat com/excel/runphreeqc.xls com/excel/withcallback.xls '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/com/excel'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/com/python'
 /data/data/com.termux/files/usr/bin/install -c -m 644 com/python/Gypsum.py com/python/parallel_advect.py com/python/phreeqc.dat com/python/pitzer.dat com/python/wateq4f.dat '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/com/python'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/cpp/advect'
 /data/data/com.termux/files/usr/bin/install -c -m 644 cpp/advect/advect.cpp cpp/advect/ic cpp/advect/phreeqc.dat '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/cpp/advect'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/fortran/advect'
 /data/data/com.termux/files/usr/bin/install -c -m 644 fortran/advect/advect.F90 fortran/advect/ic fortran/advect/phreeqc.dat '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/examples/fortran/advect'
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples'
Making install in doc
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
make[2]: Nothing to be done for 'install-exec-am'.
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc'
 /data/data/com.termux/files/usr/bin/install -c -m 644 NOTICE Phreeqc_2_1999_manual.pdf Phreeqc_3_2013_manual.pdf README RELEASE IPhreeqc.pdf '/data/data/com.termux/files/usr/local/share/doc/iphreeqc'
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/html'
 /data/data/com.termux/files/usr/bin/install -c -m 644 ../doc/html/IPhreeqc_8h.html ../doc/html/IPhreeqc_8h_source.html ../doc/html/IPhreeqc_8hpp.html ../doc/html/IPhreeqc_8hpp_source.html ../doc/html/Var_8h.html ../doc/html/Var_8h_source.html ../doc/html/bc_s.png ../doc/html/bdwn.png ../doc/html/classIPhreeqc.html ../doc/html/classIPhreeqc.png ../doc/html/classIPhreeqcStop.html ../doc/html/classIPhreeqcStop.png ../doc/html/closed.png ../doc/html/dir_68267d1309a1af8e8297ef4c3efbcdba.html ../doc/html/doxygen.css ../doc/html/doxygen.png ../doc/html/dynsections.js ../doc/html/ftv2blank.png ../doc/html/ftv2doc.png ../doc/html/ftv2folderclosed.png ../doc/html/ftv2folderopen.png ../doc/html/ftv2lastnode.png ../doc/html/ftv2link.png ../doc/html/ftv2mlastnode.png ../doc/html/ftv2mnode.png ../doc/html/ftv2node.png ../doc/html/ftv2plastnode.png ../doc/html/ftv2pnode.png ../doc/html/ftv2splitbar.png ../doc/html/ftv2vertline.png ../doc/html/index.html ../doc/html/jquery.js ../doc/html/nav_f.png ../doc/html/nav_g.png ../doc/html/nav_h.png ../doc/html/open.png ../doc/html/structVAR.html ../doc/html/sync_off.png ../doc/html/sync_on.png ../doc/html/tab_a.png '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/html'
 /data/data/com.termux/files/usr/bin/install -c -m 644 ../doc/html/tab_b.png ../doc/html/tab_h.png ../doc/html/tab_s.png ../doc/html/tabs.css '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/html'
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/doc'
Making install in database
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
make[2]: Nothing to be done for 'install-exec-am'.
 /data/data/com.termux/files/usr/bin/mkdir -p '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/database'
 /data/data/com.termux/files/usr/bin/install -c -m 644 Amm.dat ColdChem.dat core10.dat frezchem.dat iso.dat llnl.dat minteq.dat minteq.v4.dat phreeqc.dat pitzer.dat sit.dat Tipping_Hurley.dat wateq4f.dat '/data/data/com.termux/files/usr/local/share/doc/iphreeqc/database'
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/database'
Making install in gtest
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/gtest'
make[1]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'
make[2]: Entering directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'
make[1]: Leaving directory '/data/data/com.termux/files/home/iphreeqc-3.7.3-15968'

While loading library it gives this error

python Gypsum_nonCOM.py
Traceback (most recent call last):
  File "/data/data/com.termux/files/home/iphreeqc-3.7.3-15968/examples/com/python/Gypsum_nonCOM.py", line 7, in <module>
    phreeqc = phreeqc_mod.IPhreeqc('/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so')
  File "/data/data/com.termux/files/usr/lib/python3.9/site-packages/phreeqpy/iphreeqc/phreeqc_dll.py", line 51, in __init__
    phreeqc = ctypes.cdll.LoadLibrary(dll_path)
  File "/data/data/com.termux/files/usr/lib/python3.9/ctypes/__init__.py", line 452, in LoadLibrary
    return self._dlltype(name)
  File "/data/data/com.termux/files/usr/lib/python3.9/ctypes/__init__.py", line 374, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen failed: cannot locate symbol "__trunctfdf2" referenced by "/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so"...

Android .so check

readelf -dWn /data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so

Dynamic section at offset 0x2119c8 contains 29 entries:
  Tag        Type                         Name/Value
 0x000000000000001d (RUNPATH)            Library runpath: [/data/data/com.termux/files/usr/lib]
 0x0000000000000001 (NEEDED)             Shared library: [libc++_shared.so]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so]
 0x0000000000000001 (NEEDED)             Shared library: [libdl.so]
 0x000000000000000e (SONAME)             Library soname: [libiphreeqc-3.7.3.so]
 0x000000000000001e (FLAGS)              BIND_NOW
 0x000000006ffffffb (FLAGS_1)            Flags: NOW
 0x0000000000000007 (RELA)               0x3fe18
 0x0000000000000008 (RELASZ)             26712 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000006ffffff9 (RELACOUNT)          505
 0x0000000000000017 (JMPREL)             0x46670
 0x0000000000000002 (PLTRELSZ)           45984 (bytes)
 0x0000000000000003 (PLTGOT)             0x214130
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000006 (SYMTAB)             0x308
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000005 (STRTAB)             0x163a4
 0x000000000000000a (STRSZ)              170612 (bytes)
 0x000000006ffffef5 (GNU_HASH)           0x12040
 0x0000000000000019 (INIT_ARRAY)         0x2138f0
 0x000000000000001b (INIT_ARRAYSZ)       216 (bytes)
 0x000000000000001a (FINI_ARRAY)         0x2138e0
 0x000000000000001c (FINI_ARRAYSZ)       16 (bytes)
 0x000000006ffffff0 (VERSYM)             0x10a00
 0x000000006ffffffe (VERNEED)            0x11fec
 0x000000006fffffff (VERNEEDNUM)         2
 0x0000000000000000 (NULL)               0x0

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defencedog commented 11 months ago

Furher findings, the error is loading .so

>>> from ctypes import *
>>> cdll.LoadLibrary('/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/data/data/com.termux/files/usr/lib/python3.9/ctypes/__init__.py", line 452, in LoadLibrary
    return self._dlltype(name)
  File "/data/data/com.termux/files/usr/lib/python3.9/ctypes/__init__.py", line 374, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen failed: cannot locate symbol "__trunctfdf2" referenced by "/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so"...
defencedog commented 11 months ago

Solved loading issue, recompile with gcc-11 instead of clang In termux pkg i gcc-default-11 above steps / log remains same... ./configure --prefix=$PREFIX/local && make -j4 && make install 2>&1 | tee iphreeqc-3.7.3-15968_aarch64.log You can make clang default again by pkg remove gcc-default-11

Successfully run following .py (modified for nonCOM)

"""Compares gypsum solubility for WATEQ4F and Pitzer databases.
"""
# Import standard library modules first.
import os
# Import mode non-COM for LINUX / ANDROID
import phreeqpy.iphreeqc.phreeqc_dll as phreeqc_mod
phreeqc = phreeqc_mod.IPhreeqc('/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so')

# Then get third party modules.
import matplotlib.pyplot as plt

def selected_array(db_path, input_string):
    """Load database via non-COM and run input string.
    """
    phreeqc.load_database(db_path)
    phreeqc.run_string(input_string)
    return phreeqc.get_selected_output_array()

def show_results(input_string):
    """Get results for different databases
    """
    wateq4f_result = selected_array('wateq4f.dat', input_string)
    pitzer_result  = selected_array('pitzer.dat', input_string)
    # Get data from the arrays.
    nacl_conc      = [entry[0] for entry in wateq4f_result][1:]
    wateq4f_values = [entry[1] for entry in wateq4f_result][1:]
    pitzer_values  = [entry[1] for entry in pitzer_result][1:]
    # Plot
    plt.plot(nacl_conc, pitzer_values, 'k', nacl_conc, wateq4f_values,'k--')
    plt.axis([0, 6, 0, .06])
    plt.legend(('PITZER','WATEQ4F'), loc = (0.4, 0.4))
    plt.ylabel('GYPSUM SOLUBILITY, MOLES PER KILOGRAM WATER')
    plt.xlabel('NaCl, MOLES PER KILOGRAM WATER')
    plt.savefig("Figure2.png")
    plt.show()

if __name__ == '__main__':
    # This will only run when called as script from the command line
    # and not when imported from another script.
    INPUT_STRING = """
    SOLUTION 1
    END
    INCREMENTAL_REACTIONS
    REACTION
        NaCl 1.0
        0 60*0.1 moles
    EQUILIBRIUM_PHASES
        Gypsum
    USE solution 1
    SELECTED_OUTPUT
        -reset false
        -total Na S(6)
    END"""
    show_results(INPUT_STRING)

And this multi-threading example again modified

# -*- coding: utf-8 -*-

"""A coupled advection-reaction model using the COM server.

The sketch below. shows the setup. The coupled model contains a advection and a
reaction model. The reaction model can have one or more Phreeqc calculators.
The calculators can work in parallel using the module `multiprocessing`.

+--------------------------------------------------------------------------+
|                            CoupledModel                                  |
|  +--------------------------------------------------------------------+  |
|  |                         AdvectionModel                             |  |
|  |                                                                    |  |
|  +--------------------------------------------------------------------+  |
|  |                         ReactionModel                              |  |
|  |  +--------------------+--------------------+--------------------+  |  |
|  |  | PhreeqcCalculator1 | PhreeqcCalculator2 | PhreeqcCalculator3 |  |  |
+--------------------------------------------------------------------------+

Author: Mike Müller, mmueller@hydrocomputing.com
"""

import multiprocessing
import os
import time

import matplotlib.pyplot as plt
import phreeqpy.iphreeqc.phreeqc_dll as phreeqc_mod
phreeqc = phreeqc_mod.IPhreeqc('/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so')

class CoupledModel(object):
    """This is a coupled advection model.

    Since it is just a simple example, we use a 1D model.
    The same approach can be applied to a 2d or 3D model
    as long as the advection model supports it.
    The PHREEQC part is the same.
    Furthermore, instead of a simple advection model,
    we can have a more sophisticated transport model.
    """

    def __init__(self, ncells, nshifts, initial_conditions, processes):
        self.nshifts = nshifts
        self.reaction_model = ReactionModel(ncells, initial_conditions,
                                            processes)
        self.reaction_model.make_initial_state()
        init_conc = dict([(name, [value] * ncells) for name, value in
                          self.reaction_model.init_conc.items()])
        self.advection_model = AdvectionModel(init_conc,
                                              self.reaction_model.inflow_conc)
        self.component_names = self.reaction_model.component_names
        self.results = {}
        for name in self.component_names:
            self.results[name] = []

    def run(self):
        """Go over all time steps (shifts).
        """
        for shift in range(self.nshifts):
            self.advection_model.advect()
            self.advection_model.save_results(self.results)
            self.reaction_model.modify(self.advection_model.conc)
            self.advection_model.update_conc(self.reaction_model.conc)
        self.reaction_model.finish()

class AdvectionModel(object):
    """Very simple 1D advection model.

    This model can be replaced by a more sophisticated transport
    model with two or three dimensions.
    This could be an external code such as MT3D or anything
    else that is moving concentrations through the subsurface.
    """

    def __init__(self, init_conc, inflow_conc):
        """Set the initial and inflow concentrations.

        Both concentrations are dictionaries with the specie names as keys.
        Values are 1D arrays for `init_conc` and scalars for `inflow_conc`.
        """
        self.conc = init_conc
        self.inflow_conc = inflow_conc
        self.outflow = {}

    def update_conc(self, new_conc):
        """Update the concentrations after the reactions step.

        This is very simple but could be more involved
        if the transport model is more complex.
        """
        self.conc = new_conc

    def advect(self):
        """Shift one cell.
        """
        for name in self.conc:
            self.outflow[name] = self.conc[name][-1]
            self.conc[name][1:] = self.conc[name][:-1]
            self.conc[name][0] = self.inflow_conc[name]

    def save_results(self, results):
        """Save the calculation results.

        Typically, we would write our results into a file.
        For simplicity we just add the current outflow that
        we stored in `self.outflow` and add it to `results`,
        which is a dictionary with all specie names as keys
        and lists as values.
        """
        for name in self.conc:
            results[name].append(self.outflow[name])

class ReactionModel(object):
    """Calculate reactions using PHREEQC as computational engine.

    We have no direct contact with IPhreeqc here.
    We make one or more instances of `PhreeqcCalculator`
    that are actually using IPhreeqc.
    We can use more than one processor with `multiprocessing`.
    """

    def __init__(self, ncells, initial_conditions, processes):
        if processes > ncells:
            raise ValueError('Number of processes needs to be less or equal '
                             'than number of cells. %d processes %d cells.'
                             % (processes, ncells))
        if processes < 1:
            raise ValueError('Need at least one process got %d' % processes)
        self.parallel = False
        if processes > 1:
            self.parallel = True
        self.ncells = ncells
        self.initial_conditions = initial_conditions
        self.processes = processes
        self.inflow_conc = {}
        self.init_conc = {}
        self.conc = {}
        self.component_names = []
        self.calculators = []
        self.cell_ranges = []
        self._init_calculators()
        self.make_initial_state()

    def _init_calculators(self):
        """If we are going parallel we need several calculators.
        """
        if self.parallel:
            # Domain decomposition.
            slave_ncells, reminder = divmod(self.ncells, self.processes)
            root_ncells = slave_ncells + reminder
            current_cell = root_ncells
            root_calculator = PhreeqcCalculator(root_ncells,
                                                self.initial_conditions)
            self.calculators = [root_calculator]
            self.cell_ranges = [(0, root_ncells)]
            for process in range(self.processes - 1):
                self.calculators.append(PhreeqcCalculatorProxy(slave_ncells,
                                                    self.initial_conditions))
                self.cell_ranges.append((current_cell,
                                         current_cell + slave_ncells))
                current_cell += slave_ncells
            assert current_cell == self.ncells
            self.calculators.reverse()
            self.cell_ranges.reverse()
        else:
            root_calculator = PhreeqcCalculator(self.ncells,
                                                self.initial_conditions)
            # Just one calculator and the entire range but still use a list
            # to provide the same interface as the parallel case.
            self.calculators = [root_calculator]
            self.cell_ranges = [(0, self.ncells)]

    def make_initial_state(self):
        """Get the initial values from the calculator(s).
        """
        self.inflow_conc = self.calculators[0].inflow_conc
        self.init_conc = self.calculators[0].init_conc
        self.component_names = self.calculators[0].component_names
        if self.parallel:
            # Make sure all calculators are initialized the same.
            for calculator in self.calculators[1:]:
                assert self.inflow_conc == calculator.inflow_conc
                assert self.init_conc == calculator.init_conc
                assert self.component_names == calculator.component_names

    def modify(self, new_conc):
        """Pass new conc after advection to the calculator.
        """
        self.conc = {}
        for name in self.component_names:
            self.conc[name] = []
        for cell_range, calculator in zip(self.cell_ranges, self.calculators):
            current_conc = dict([(name, value[cell_range[0]:cell_range[1]]) for
                                  name, value in new_conc.items()])
            calculator.modify(current_conc)
        for calculator in self.calculators:
            conc = calculator.get_modified()
            for name in self.component_names:
                self.conc[name].extend(conc[name])

    def finish(self):
        """This is necessary for multiprocessing.

        Multiprocessing uses external processes. These need to be
        explicitly closed to avoid hanging of the program at
        the end.
        """
        for calculator in self.calculators:
            calculator.finish()

class PhreeqcCalculator(object):
    """All PHREEQC calculations happen here.

    This is the only place where we interact wit IPhreeqc.
    Each instance of this class might run in a different
    process using `multiprocessing`.
    """

    def __init__(self, ncells, initial_conditions):
        """
        ncells - number of cells
        initial_conditions - string containing PHREEQC input for
                             solution and exchange, see example below
        """
        self.ncells = ncells
        self.initial_conditions = initial_conditions
        self.inflow_conc = {}
        self.init_conc = {}
        self.conc = {}
        self.phreeqc = phreeqc_mod.IPhreeqc('/data/data/com.termux/files/usr/local/lib/libiphreeqc-3.7.3.so')
        self.phreeqc.load_database(r"phreeqc.dat")
        self.components = []
        self.component_names = []
        self._make_initial_state()

    def _make_initial_state(self):
        """Copy solution to all cells and calculate initial conditions.
        """
        self.phreeqc.run_string(self.initial_conditions)
        self.components = self.phreeqc.get_component_list()
        start = 1
        end = self.ncells
        code = ''
        code += "COPY solution 1 %d-%d\n" % (start, end)
        code += "COPY exchange 1 %d-%d\n" % (start, end)
        code += "END\n"
        code += "RUN_CELLS; -cells %d-%d\n" % (start, end)
        code += self.make_selected_output(self.components)
        self.phreeqc.run_string(code)
        self.conc = self.get_selected_output()
        all_names = self.conc.keys()
        self.component_names = [name for name in all_names if name not in
                                ('cb', 'H', 'O')]
        code = ''
        code += self.make_selected_output(self.components)
        code += "RUN_CELLS; -cells 0-1\n"
        self.phreeqc.run_string(code)
        start_conc = self.get_selected_output()
        for name in self.component_names:
            self.inflow_conc[name] = start_conc[name][0]
            self.init_conc[name] = start_conc[name][1]

    def modify(self, new_conc):
        """Set new concentration after advection and re-calculate.
        """
        conc = self.conc
        end = self.ncells + 1
        conc.update(new_conc)
        modify = []
        for index, cell in enumerate(range(1, end)):
            modify.append("SOLUTION_MODIFY %d" % cell)
            modify.append("\t-cb      %e" % conc['cb'][index])
            modify.append("\t-total_h %s" % conc['H'][index])
            modify.append("\t-total_o %s" % conc['O'][index])
            modify.append("\t-totals")
            for name in self.component_names:
                modify.append("\t\t%s\t%s" % (name, conc[name][index]))
        modify.append("RUN_CELLS; -cells %d-%d\n" % (1, self.ncells))
        code = '\n'.join(modify)
        self.phreeqc.run_string(code)
        self.conc = self.get_selected_output()

    def get_modified(self):
        """Return calculated conc.
        """
        return self.conc

    @ staticmethod # this is just a function but belongs here
    def make_selected_output(components):
        """
        Build SELECTED_OUTPUT data block.
        """
        headings = "-headings    cb    H    O    "
        headings += '\t'.join(components)
        selected_output = """
        SELECTED_OUTPUT
            -reset false
        USER_PUNCH
        """
        selected_output += headings + "\n"
        # charge balance, H, and O
        code = '10 w = TOT("water")\n'
        code += '20 PUNCH CHARGE_BALANCE, TOTMOLE("H"), TOTMOLE("O")\n'
        # All other elements
        lino = 30
        for component in components:
            code += '%d PUNCH w*TOT(\"%s\")\n' % (lino, component)
            lino += 10
        selected_output += code
        return selected_output

    def get_selected_output(self):
        """Return calculation result as dict.

        Header entries are the keys and the columns
        are the values as lists of numbers.
        """
        output = self.phreeqc.get_selected_output_array()
        header = output[0]
        conc = {}
        for head in header:
            conc[head] = []
        for row in output[1:]:
            for col, head in enumerate(header):
                conc[head].append(row[col])
        return conc

    def finish(self):
        """Placeholder to give same interface as the multiprocessing version.
        """
        pass

class PhreeqcCalculatorProxy(object):
    """Proxy that communicates with other processes.

    We uses this proxy for parallel computations.
    All code that is specific for parallel computing is located
    in here.
    """

    def __init__(self, ncells, initial_conditions):
        """Go parallel.
        """
        self.in_queue = multiprocessing.JoinableQueue()
        self.out_queue = multiprocessing.JoinableQueue()
        self.process = multiprocessing.Process(
            target=process_worker,
            args=(ncells, initial_conditions, self.in_queue, self.out_queue))
        self.process.start()
        (self.inflow_conc,
         self.init_conc,
         self.component_names) = self.out_queue.get()

    def modify(self, new_conc):
        """Run PHREEQC in another process.
        """
        self.in_queue.put(new_conc)

    def get_modified(self):
        """Return calculated conc.
        """
        return self.out_queue.get()

    def finish(self):
        """Terminate the process.
        """
        self.in_queue.put(None)
        self.process.join()

def process_worker(ncells, initial_conditions, in_queue, out_queue):
    """This runs in another process.
    """
    print ('Started process with ID', os.getpid())
    calculator = PhreeqcCalculator(ncells, initial_conditions)
    out_queue.put((calculator.inflow_conc, calculator.init_conc,
                  calculator.component_names))
    while True:
        new_conc = in_queue.get()
        # None is the sentinel. We are done
        if new_conc is None:
            break
        calculator.modify(new_conc)
        out_queue.put(calculator.conc)

def plot(ncells, outflow, specie_names):
    """Plot the results.
    """
    colors = {'Ca': 'r', 'Cl': 'b', 'K': 'g', 'N': 'y', 'Na': 'm'}
    x = [i / float(ncells) for i in
         range(1, len(outflow[specie_names[0]]) + 1)]
    args = []
    for name in specie_names:
        args.extend([x, outflow[name], colors[name]])
    # pylint: disable-msg=W0142
    # we do want *
    plt.plot(*args)
    plt.legend(specie_names, loc=(0.8, 0.5))
    plt.ylabel('MILLIMOLES PER KILOGRAM WATER')
    plt.xlabel('PORE VOLUME')
    plt.show()

def measure_time(func, *args, **kwargs):
    """Convenience function to measure run times.
    """
    import sys
    if sys.platform == 'win32':
        # time.clock is more accurate on Windows
        # deprecation warning
        timer_func = time.clock
    else:
        # but behaves differently on other platforms
        timer_func = time.process_time
    start = timer_func()
    result = func(*args, **kwargs)
    return result, time.process_time() - start

if __name__ == '__main__':

    def main(ncells, nshifts, processes=2):
        """
        Specify initial conditions data blocks.

        Uniform initial conditions are assumed.
        """
        initial_conditions = """
        TITLE Example 11.--Transport and ion exchange.
        SOLUTION 0  CaCl2
            units            mmol/kgw
            temp             25.0
            pH               7.0     charge
            pe               12.5    O2(g)   -0.68
            Ca               0.6
            Cl               1.2
        SOLUTION 1  Initial solution for column
            units            mmol/kgw
            temp             25.0
            pH               7.0     charge
            pe               12.5    O2(g)   -0.68
            Na               1.0
            K                0.2
            N(5)             1.2
            END
        EXCHANGE 1
            equilibrate 1
            X                0.0011
        END
            """

        def run():
            """Do the work.
            """
            model = CoupledModel(ncells, nshifts, initial_conditions,
                                 processes)
            model.run()
            return model, model.results
        (model, outflow), run_time = measure_time(run)
        print ('Statistics')
        print ('==========')
        print ('number of cells:    ', ncells)
        print ('number of shifts:   ', nshifts)
        print ('number of processes:', processes)
        print ('run_time:           ', run_time)
        plot(ncells, outflow, model.component_names)

    main(ncells=400, nshifts=1200, processes=2)

results

~/.../com/python $ python parallel_advect_nonCOM.py
Started process with ID 11153
Statistics
==========
number of cells:     400
number of shifts:    1200
number of processes: 2
run_time:            34.015152873999995