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

[Saumil Patel]

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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