[MOAB-dev] Building MOAB from Scratch: Error when I run 'make'

[Saumil Patel]

Thanks, Rajeev. That fixed the problem.


On Wed, Jun 18, 2014 at 12:42 PM, Rajeev Jain <jain at mcs.anl.gov> wrote:

> It seems like #include <time.h> is missing from MBZoltan.hpp.
> Please try adding it.
>
> Rajeev
>
>   ------------------------------
>  *From:* Saumil Patel <saumil.patel134 at gmail.com>
> *To:* "moab-dev at mcs.anl.gov" <moab-dev at mcs.anl.gov>
> *Sent:* Wednesday, June 18, 2014 11:18 AM
> *Subject:* [MOAB-dev] Building MOAB from Scratch: Error when I run 'make'
>
>    Dear Moab-Dev Community,
>
>  I am building MOAB from scratch on a cluster. I am using the following
> command './configure' command:
>
> ./configure --with-mpi --with-hdf5=<hdf5-location> --enable-mbzoltan --with-zoltan=<zoltan_dir>
>
> As you can see, I am using MOAB with hdf5 and Zoltan.  I am using a PGI
> compiler.  After I am done with the configure, I execute the 'make' command
> and get the following errors:
>
>  $ make
>
> make  all-recursive
> make[1]: Entering directory `/home/sharedlib/moab-4.6.3'
> Making all in src
> make[2]: Entering directory `/home/sharedlib/moab-4.6.3/src'
> make  all-recursive
> make[3]: Entering directory `/home/sharedlib/moab-4.6.3/src'
> Making all in parallel
> make[4]: Entering directory `/home/sharedlib/moab-4.6.3/src/parallel'
> make  all-am
> make[5]: Entering directory `/home/sharedlib/moab-4.6.3/src/parallel'
> make[5]: Leaving directory `/home/sharedlib/moab-4.6.3/src/parallel'
> make[4]: Leaving directory `/home/sharedlib/moab-4.6.3/src/parallel'
> Making all in io
> make[4]: Entering directory `/home/sharedlib/moab-4.6.3/src/io'
> Making all in mhdf
> make[5]: Entering directory `/home/sharedlib/moab-4.6.3/src/io/mhdf'
> make[5]: Nothing to be done for `all'.
> make[5]: Leaving directory `/home/sharedlib/moab-4.6.3/src/io/mhdf'
> Making all in .
> make[5]: Entering directory `/home/sharedlib/moab-4.6.3/src/io'
> make[5]: Nothing to be done for `all-am'.
> make[5]: Leaving directory `/home/sharedlib/moab-4.6.3/src/io'
> make[4]: Leaving directory `/home/sharedlib/moab-4.6.3/src/io'
> Making all in LocalDiscretization
> make[4]: Entering directory
> `/home/sharedlib/moab-4.6.3/src/LocalDiscretization'
> make[4]: Nothing to be done for `all'.
> make[4]: Leaving directory
> `/home/sharedlib/moab-4.6.3/src/LocalDiscretization'
> Making all in .
> make[4]: Entering directory `/home/sharedlib/moab-4.6.3/src'
> \
>     source='./../tools/mbzoltan/MBZoltan.cpp' object='MBZoltan.lo'
> libtool=yes \
>     DEPDIR=.deps depmode=none /bin/sh ../config/depcomp \
>     /bin/sh ../libtool  --tag=CXX   --mode=compile mpiCC -DHAVE_CONFIG_H
> -I. -I.. -I../src/moab -I../src/parallel
> -I/home/sharedlib/hdf5_parallel_build/hdf5/include
> -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF
> -D_FILE_OFFSET_BITS=64   -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL
> -DHAVE_ZOLTAN -I./parallel -DIS_BUILDING_MB -I. -I./io -I./io/mhdf/include
> -I./parallel -I./LocalDiscretization -I/home/sharedlib/Zoltan_v3.8/    -O2
> -DNDEBUG -c -o MBZoltan.lo `test -f './../tools/mbzoltan/MBZoltan.cpp' ||
> echo './'`./../tools/mbzoltan/MBZoltan.cpp
> libtool: compile:  mpiCC -DHAVE_CONFIG_H -I. -I.. -I../src/moab
> -I../src/parallel -I/home/sharedlib/hdf5_parallel_build/hdf5/include
> -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF
> -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DHAVE_ZOLTAN
> -I./parallel -DIS_BUILDING_MB -I. -I./io -I./io/mhdf/include -I./parallel
> -I./LocalDiscretization -I/home/sharedlib/Zoltan_v3.8/ -O2 -DNDEBUG -c
> ./../tools/mbzoltan/MBZoltan.cpp -o MBZoltan.o
> "./../tools/mbzoltan/MBZoltan.cpp", line 254: *error*: identifier
> "clock_t" is
>           undefined
>     clock_t t = clock();
>     ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 254: *error*: identifier "clock"
> is
>           undefined
>     clock_t t = clock();
>                 ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 338: *error*: identifier
>           "CLOCKS_PER_SEC" is undefined
>       std::cout << " time to LB_partition " << (clock() - t) / (double)
> CLOCKS_PER_SEC  << "s. \n";
>                                                                         ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 380: *error*: identifier
> "clock_t" is
>           undefined
>     clock_t t = clock();
>     ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 380: *error*: identifier "clock"
> is
>           undefined
>     clock_t t = clock();
>                 ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 472: *error*: identifier
>           "CLOCKS_PER_SEC" is undefined
>       std::cout << " time to assemble graph: " << (clock() - t) / (double)
> CLOCKS_PER_SEC  << "s. \n";
>
> ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 490: *error*: identifier
>           "CLOCKS_PER_SEC" is undefined
>       std::cout << " time to initialize points: " << (clock() - t) /
> (double) CLOCKS_PER_SEC  << "s. \n";
>
> ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 592: *error*: identifier
>           "CLOCKS_PER_SEC" is undefined
>       std::cout << " time to LB_partition " << (clock() - t) / (double)
> CLOCKS_PER_SEC  << "s. \n";
>                                                                         ^
>
> "./../tools/mbzoltan/MBZoltan.cpp", line 612: *error*: identifier
>           "CLOCKS_PER_SEC" is undefined
>       std::cout << " time to write partition in memory " <<(clock() - t) /
> (double) CLOCKS_PER_SEC  << "s. \n";
>
> ^
>
> 9 *errors* detected in the compilation of
> "./../tools/mbzoltan/MBZoltan.cpp".
>
>  Has anyone encountered these problems? If so, can you recommend something
> I can do to fix it?  Your help is greatly appreciated.
>
>  Best,
>
>  Saumil
>
>
>
>
>
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