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updated the guidance document
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‎KNOWN_ISSUES.txt

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large malloc problem
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====================
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Description
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-----------
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alquimia >= r144 8e9ef8e, <= r148
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running: batch_chem -i general-reaction-pc.cfg -d
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alquimia <= r143 2e6ed9f
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running: batch_chem -i general-reaction-ac.cfg -d
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cause an attempt to malloc huge (~1.3-1.8GB) of memory during a
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function call in pflotran:database_module%basisinit to
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database_aux_module%DatabaseRxnCreateFromRxnString at
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~database.F90:2898
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screen output
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~~~~~~~~~~~~~
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PFloTran_Alquimia_Setup() :
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Reading : general-reaction.in
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WARNING: Card (NONISOTHERMAL) not found in input file.batch_chem(48324) malloc: *** mmap(size=132224767150366720) failed (error code=12)
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*** error: can't allocate region
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*** set a breakpoint in malloc_error_break to debug
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Operating system error: Cannot allocate memory
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Memory allocation failed
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backtrace
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~~~~~~~~~
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#5 0x00007fff97f9d1b3 in malloc_zone_malloc ()
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from /usr/lib/system/libsystem_c.dylib
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#6 0x00007fff97f9dc07 in malloc () from /usr/lib/system/libsystem_c.dylib
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#7 0x00000001004335a9 in _gfortrani_get_mem ()
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from /opt/local/lib/gcc46/libgfortran.3.dylib
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#8 0x000000010050a1b0 in _gfortran_internal_pack ()
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from /opt/local/lib/gcc46/libgfortran.3.dylib
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#9 0x000000010005eafb in __database_module_MOD_basisinit (reaction=...,
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option=...) at database.F90:2898
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#10 0x000000010000eb84 in __pflotranalquimiainterface_module_MOD_initializepflotranreactions (option=0x101020a00, input=0x101022400, reaction=0x101028c00)
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at pflotran_alquimia_interface.F90:902
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#11 0x000000010001123f in __pflotranalquimiainterface_module_MOD_setup (
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input_filename=..., pft_engine_state=0x400, sizes=..., functionality=...,
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status=..., _input_filename=1) at pflotran_alquimia_interface.F90:163
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#12 0x00000001000115b7 in pflotran_alquimia_setup (input_filename=...,
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pft_engine_state=0x400, sizes=..., functionality=..., status=...)
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at pflotran_alquimia_wrappers.F90:46
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#13 0x0000000100002924 in BatchChemWithAlquimia (demo_simulation=...,
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demo_state=..., demo_material_props=..., demo_conditions=...,
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output=<optimized out>) at batch_chem.cc:176
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Notes
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-----
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* Using Mac OS X 10.8.4, gcc 4.7.3, mpich-3.0.4, I've worked back
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through the alquimia history from r143(2e6ed9f)--r112(57432fd) and
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general-reaction-ac.cfg exhibits this error in all versions.
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* Not using the debug flag '-d' does not generate this error. Harding
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coding the internal debug flag to on and leaving the command line flag
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off does not generate this error. --> implies an issue with command
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line processing.
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* getopt, petsc, and mpi all touch the command line flags.
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* Commenting out the getopt calls and simply hard coding the values,
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passing no command line args --> ok. passing command line args -->
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fails. Not a problem with getopt
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* passing command line args and using PetscInitializeNoArguements() -->
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ok, appears to be a problem with petsc or mpi commandline processing.
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* passing commandline args but adding a call to
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PetscOptionsView(PETSC_STDOUT_VIEWER?) immediately after
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PetscInitialize() --> ok. Moving PetscOptionsView(...) down eventually
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causes the same error when it comes after cfg_reader.ReadInputFile().
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* Doing commandline processing in petsc using PetscOptionsGetXXX()
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seems to side step this problem with when running
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general-reaction-pc.cfg with debug. It's not clear if this
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actually fixes the problem, or is a bandaid like the
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PetscOptionsView() described above. This "fix" will be committed
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as r149 as part of the work to remove getopt/xgetopt.
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Platform Status
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---------------
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Mac OS X
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~~~~~~~~
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alquimia(639283b202dd) : pflotran(8083548d3f59) : petsc(61d360f)
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mpich-3.0.4-106
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openmpi-1.6.4
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gcc46 @4.6.4_1
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gcc47 @4.7.3_1
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gcc48 @4.8.1_1
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Darwin 12.4.0 = OS X v10.8.4
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PASS : gcc4.6-openmpi-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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FAIL : gcc4.6-mpich-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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PASS : gcc4.7-openmpi-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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FAIL : gcc4.7-mpich-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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PASS : gcc4.8-openmpi-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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PASS : gcc4.8-mpich-gr-pc : Darwin 12.4.0 : Xcode 4.6.3
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Darwin 11.4.2 = Mac OS X v10.7.5
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PASS : gcc4.6-openmpi-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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PASS : gcc4.6-mpich-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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PASS : gcc4.7-openmpi-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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PASS : gcc4.7-mpich-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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PASS : gcc4.8-openmpi-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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PASS : gcc4.8-mpich-gr-pc : Darwin 11.4.2 : Xcode 4.4.1
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Linux Mint 14 Nadia
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~~~~~~~~~~~~~~~~~~~

‎LICENSE.txt

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Alquimia Copyright (c) 2013, The Regents of the University of
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California, through Lawrence Berkeley National Laboratory (subject to
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receipt of any required approvals from the U.S. Dept. of Energy). All
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rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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(1) Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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(2) Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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(3) Neither the name of the University of California, Lawrence
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Berkeley National Laboratory, U.S. Dept. of Energy nor the names of
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its contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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You are under no obligation whatsoever to provide any bug fixes,
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patches, or upgrades to the features, functionality or performance of
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the source code ("Enhancements") to anyone; however, if you choose to
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make your Enhancements available either publicly, or directly to
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Lawrence Berkeley National Laboratory, without imposing a separate
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written license agreement for such Enhancements, then you hereby grant
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the following license: a non-exclusive, royalty-free perpetual license
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to install, use, modify, prepare derivative works, incorporate into
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other computer software, distribute, and sublicense such enhancements
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or derivative works thereof, in binary and source code form.

‎README.rst

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Legal
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-----
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"Alquimia Copyright (c) 2013, The Regents of the University of
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California, through Lawrence Berkeley National Laboratory (subject to
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receipt of any required approvals from the U.S. Dept. of Energy). All
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rights reserved.
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If you have questions about your rights to use or distribute this
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software, please contact Berkeley Lab's Technology Transfer and
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Intellectual Property Management at [email protected] referring to "Alquimia
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(LBNL Ref. 2013-119)."
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NOTICE. This software was developed under funding from the
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U.S. Department of Energy. As such, the U.S. Government has been
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granted for itself and others acting on its behalf a paid-up,
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nonexclusive, irrevocable, worldwide license in the Software to
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reproduce, prepare derivative works, and perform publicly and display
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publicly. Beginning five (5) years after the date permission to
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assert copyright is obtained from the U.S. Department of Energy, and
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subject to any subsequent five (5) year renewals, the U.S. Government
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is granted for itself and others acting on its behalf a paid-up,
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nonexclusive, irrevocable, worldwide license in the Software to
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reproduce, prepare derivative works, distribute copies to the public,
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perform publicly and display publicly, and to permit others to do so.
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Description
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-----------
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Alquimia is an biogeochemistry API and wrapper library being developed
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as part of the [ASCEM](http://esd.lbl.gov/research/projects/ascem/)
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project.
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The aim is to provide a unified interface to existing "geochemistry
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engines" such as
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[CrunchFlow](http://www.csteefel.com/CrunchFlowIntroduction.html) or
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[PFLOTRAN](https://bitbucket.org/pflotran/pflotran-dev), allowing
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subsurface flow and transport simulators to access a range of
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functionality.
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It is not an implementation of a biogeochemistry reaction library, and
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does not do any geochemical calculations.
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Building
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--------
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To build alquimia, you must have petsc installed, with the PETSC_DIR
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and PETSC_ARCH environment variables set. Compilers are obtained from
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the petsc variables.
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PFLOTRAN_DIR=/path/to/pflotran/dir must be defined to link pflotran.
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::
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cd ${ALQUIMIA_DIR}/src
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export PFLOTRAN_DIR=${HOME}/projects/pflotran-dev
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make all
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Test your build by running the batch chemistry demo driver.
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::
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cd ${ALQUIMIA_DIR}/tests
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ln -s ../src/drivers/batch_chem .
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./batch_chem -d -i calcite-short-pc.cfg
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Builds are debug by default. To build without debug symbols and with
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optimization:
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::
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make RELEASE=1 all
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The default compiler is assumed to be GCC (or compatible LLVM?). And
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uses GCC specific build options. To build with minimal generic build
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flags:
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::
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make COMPILER=generic all

‎alquimia/alquimia.vfproj

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<?xml version="1.0" encoding="UTF-8"?>
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<VisualStudioProject ProjectCreator="Intel Fortran" Keyword="Console Application" Version="11.0" ProjectIdGuid="{78920602-A012-416F-860F-A9B7F32CE13B}">
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<Platforms>
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<Platform Name="Win32"/></Platforms>
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<Configurations>
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<Configuration Name="Debug|Win32">
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<Tool Name="VFFortranCompilerTool" SuppressStartupBanner="true" DebugInformationFormat="debugEnabled" Optimization="optimizeDisabled" Interfaces="true" WarnInterfaces="true" Traceback="true" BoundsCheck="true" RuntimeLibrary="rtMultiThreadedDebug"/>
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<Tool Name="VFLinkerTool" LinkIncremental="linkIncrementalNo" SuppressStartupBanner="true" GenerateDebugInformation="true" SubSystem="subSystemConsole"/>
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<Tool Name="VFResourceCompilerTool"/>
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<Tool Name="VFMidlTool" SuppressStartupBanner="true"/>
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<Tool Name="VFCustomBuildTool"/>
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<Tool Name="VFPreLinkEventTool"/>
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<Tool Name="VFPreBuildEventTool"/>
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<Tool Name="VFPostBuildEventTool"/>
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<Tool Name="VFManifestTool" SuppressStartupBanner="true"/></Configuration>
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<Configuration Name="Release|Win32">
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<Tool Name="VFFortranCompilerTool" SuppressStartupBanner="true"/>
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<Tool Name="VFLinkerTool" LinkIncremental="linkIncrementalNo" SuppressStartupBanner="true" SubSystem="subSystemConsole"/>
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<Tool Name="VFResourceCompilerTool"/>
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<Tool Name="VFMidlTool" SuppressStartupBanner="true"/>
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<Tool Name="VFCustomBuildTool"/>
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<Tool Name="VFPreLinkEventTool"/>
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<Tool Name="VFPreBuildEventTool"/>
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<Tool Name="VFPostBuildEventTool"/>
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<Tool Name="VFManifestTool" SuppressStartupBanner="true"/></Configuration></Configurations>
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<Files>
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<Filter Name="Header Files" Filter="fi;fd"/>
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<Filter Name="Resource Files" Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"/>
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<Filter Name="Source Files" Filter="f90;for;f;fpp;ftn;def;odl;idl">
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<Filter Name="csource">
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<File RelativePath="..\src\alquimia\c\alquimia_constants.c"/>
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<File RelativePath="..\src\alquimia\c\alquimia_constants.h"/>
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<File RelativePath="..\src\alquimia\c\alquimia_containers.h"/>
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<File RelativePath="..\src\alquimia\c\alquimia_interface.c"/>
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<File RelativePath="..\src\alquimia\c\alquimia_interface.h"/>
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<File RelativePath="..\src\alquimia\c\alquimia_memory.c"/>
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<File RelativePath="..\src\alquimia\c\alquimia_memory.h"/>
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<File RelativePath="..\src\alquimia\c\alquimia_util.c"/>
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<File RelativePath="..\src\alquimia\c\alquimia_util.h"/>
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<File RelativePath="..\src\alquimia\c\crunch_alquimia_interface.h"/>
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<File RelativePath="..\src\alquimia\c\pflotran_alquimia_interface.h"/>
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<File RelativePath="..\src\alquimia\c\xstdbool.h"/></Filter>
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<File RelativePath="..\src\alquimia\fortran\alquimia_containers.F90"/>
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<File RelativePath="..\src\alquimia\fortran\c_f_interface_module.F90"/>
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<File RelativePath="..\src\alquimia\fortran\crunch_alquimia_interface.F90"/>
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<File RelativePath="..\src\alquimia\fortran\crunch_alquimia_wrappers.F90"/>
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<File RelativePath="..\src\alquimia\fortran\pflotran_alquimia_interface.F90"/>
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<File RelativePath="..\src\alquimia\fortran\pflotran_alquimia_wrappers.F90"/></Filter></Files>
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<Globals/></VisualStudioProject>

‎contrib/valgrind/valgrind-pflotran.supp

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{
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pflotran_input_gfortran_string_len_trim
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Memcheck:Cond
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fun:_gfortran_string_len_trim
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fun:__input_module_MOD_inputfindstringinfile1
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fun:__pflotranalquimiainterface_module_MOD_initializepflotranreactions
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fun:__pflotranalquimiainterface_module_MOD_setup
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fun:pflotran_alquimia_setup
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fun:main
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}
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{
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pflotran_database_gfortran_string_len_trim
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Memcheck:Cond
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fun:_gfortran_string_len_trim
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fun:__database_module_MOD_databaseread
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fun:__pflotranalquimiainterface_module_MOD_initializepflotranreactions
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fun:__pflotranalquimiainterface_module_MOD_setup
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fun:pflotran_alquimia_setup
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fun:main
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}
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{
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pflotran_input_readword2
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Memcheck:Cond
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fun:__input_module_MOD_inputreadword2
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fun:__constraint_module_MOD_tranconstraintread
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fun:__pflotranalquimiainterface_module_MOD_readpflotranconstraints
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fun:__pflotranalquimiainterface_module_MOD_setup
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fun:pflotran_alquimia_setup
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fun:main
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}
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{
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pflotran_database_basisinit
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Memcheck:Leak
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fun:malloc
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fun:__database_module_MOD_basisinit
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fun:__pflotranalquimiainterface_module_MOD_initializepflotranreactions
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fun:__pflotranalquimiainterface_module_MOD_setup
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fun:pflotran_alquimia_setup
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fun:main
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}

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