[CIG-SHORT] PyLith tutorial at CIG16: things you need to do before the tutorial

Mon Jun 13 08:44:46 PDT 2016

Brad,

The "=yes" in the infinite loop is not printed within the config.log, 
only in the terminal (screen).  I left config running for 15 min, and 
was still printing this string to the screen.  I had attached both the 
config.log and a stdout capture (with millions of "=yes" lines stripped 
out) to my original message - perhaps they got stripped off?  Attaching 
them again ...

Thanks,
Ravi.
====================================

On 06/13/2016 09:29 AM, Brad Aagaard wrote:
> Ravi,
>
> Please send the config.log file for the PyLith configure that is in an 
> infinite loop, so we can diagnose this further. It it is large, gzip 
> the log file.
>
> Thanks,
> Brad
>
>
> On 06/13/2016 08:13 AM, Ravi Kanda wrote:
>> Hi Brad,
>>
>> I am trying to install Pylith on Ubuntu 14 with the latest source
>> installer tarball (2.1.0-3).  I already have previous (apt-get)
>> installations of mpi2, python/numpy, netcdf4, proj4, and cppunit. So, I
>> am using the "DESKTOP-LINUX-MINIMAL" options as described in the
>> "INSTALL" file.  Running config from directory $PYLITHROOT/src/pylith,
>> which also contains the pylith installer directory,
>> 'pylith-installer-2.1.0-3'.  I am running into config problems (attached
>> CONFIG.LOG), which I hope is due to a stupid mistake on my part:
>>
>> (1) I get two "command not found" or "No such file or directory" errors
>> when I unset or set, respectively, the CPPFLAGS env variable related to
>> the following:
>>       - configure:22278: checking cppunit/TestRunner.h presence
>>       - configure:23244: checking netcdfcpp.h presence
>> The appropriate include-dir for the above on my system is /usr/include,
>> which I thought was 'standard'.  Also, in both cases, I see something
>> like the following below each of these items (line numbers purged):
>>      "... accepted by the compiler, rejected by the preprocessor!
>>       ... WARNING: ... : proceeding with the compiler's result"
>>
>> (2)  Then configure seems to go into an "infinite loop" after looking
>> for 'netcdfcpp.h', printing out lines containing only the string "=yes"
>> (see attached STDOUT capture).  When I look at system processes in
>> 'top', I see an executable with the name 'yes' running away.
>>
>> Any tips will be greatly appreciated!
>>
>> Thanks,
>> Ravi.
>> ===============================================
>>
>> On 06/06/2016 10:48 AM, Brad Aagaard wrote:
>>> PyLith Tutorial: Things you need to do **before** the tutorial
>>>
>>>   IMPORTANT: We expect you to make use of the extensive documentation
>>>   and online instructions **BEFORE** the tutorial. This will allow us
>>>   to make better use of the limited time for tutorials at the
>>>   CIG16 meeting.
>>>
>>>   1. Install PyLith, ParaView, and CUBIT/Trelis. See the instructions
>>>   at the bottom of the tutorial webpage. PyLith and Paraview are
>>>   open-source with binary packages available; Trelis has a 30-day
>>>   free trial. Some institutions may already have Trelis licenses, so
>>>   ask around your department to see if you can use an existing
>>>   license.
>>>
>>>   For the tutorial, we will be using PyLith v2.2.0, ParaView 5.0.1,
>>>   CUBIT 15.1 (US gov't agencies), and Trelis 16.0.2 (everyone
>>>   else). PyLith v2.2.0 will be released shortly before the
>>>   tutorial. It will include some bug fixes and improvements to the
>>>   manual. We recommend getting familiar with v2.1.0 as it is very
>>>   similar.
>>>
>>>   2. Read the software manuals!
>>>
>>>   3. View the videos from last year's tutorials that are available
>>>   online at https://wiki.geodynamics.org/software:pylith:start (2015
>>>   Crustal Deformation Modeling Tutorial). Work through the examples
>>>   that are discused.
>>>
>>>   4. If possible, come to the workshop with an idea of what you want
>>>   to model. In general, we recommend starting with a small, 2-D
>>>   simplified version to play with during the workshop and then
>>>   gradually adding complexity to achieve the desired final
>>>   model. Participants who follow this advice get the most out of the
>>>   tutorials!
>>>
>>> Regards,
>>> Brad Aagaard
>>> Charles Williams
>>> Matt Knepley
>>
>

-- 
---------------------------------------------------------------------
Ravi Kanda
Adjunct Assistant Professor
Department of Geology
Utah State University
4505 Old Main Hill
Logan UT 84322-4505
--------------------------
Web Page: https://ravi-vs-kanda.github.io

----------------------------------------------------------------------
For a human being, the unexamined life is not worth living - SOCRATES
----------------------------------------------------------------------

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checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
WITHVAL yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether ln -s works... yes
checking for tar... /bin/tar
checking for wget... /usr/bin/wget
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking python sysconfig... ok
checking for python include directory... /usr/include/python2.7
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking python config... ok
checking whether -lpython2.7 is a shared library... yes
checking for python module zlib... Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: 'module' object has no attribute '__file__'
found 
checking for deflate in -lz... yes
checking for mpicc... /usr/bin/mpicc
checking for mpicxx... /usr/bin/mpicxx
checking for mpif90... /usr/bin/mpif90
checking cppunit/TestRunner.h usability... yes
checking cppunit/TestRunner.h presence... no
configure: WARNING: cppunit/TestRunner.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: cppunit/TestRunner.h: proceeding with the compiler's result
checking for cppunit/TestRunner.h... yes
checking for CppUnit::TestRunner in -lcppunit... yes
checking for numpy python module... found
checking for numpy include directory... /usr/lib/python2.7/site-packages/numpy/core/include
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... yes
checking for h5dump... /usr/bin/h5dump
checking whether /usr/bin/python version is >= 2.6... yes
checking for /usr/bin/python version... (cached) 2.7
checking for /usr/bin/python platform... (cached) linux2
checking for /usr/bin/python script directory... (cached) ${prefix}/lib/python2.7/site-packages
checking for /usr/bin/python extension module directory... (cached) ${exec_prefix}/lib/python2.7/site-packages
checking netcdfcpp.h usability... yes
checking netcdfcpp.h presence... no
configure: WARNING: netcdfcpp.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: netcdfcpp.h: proceeding with the compiler's result
checking for netcdfcpp.h... yes
checking for NcFile in -lnetcdfc++... yes
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< REPEATS TO millions of lines !!! >

[CIG-SHORT] PyLith tutorial at CIG16: things you need to do **before** the tutorial

[CIG-SHORT] PyLith tutorial at CIG16: things you need to do before the tutorial