Compiler dependency

[M-K-Lee]

@dmcdougall

I tried to install ESIO-0.1.on Wrangler, TACC.

First I configured with "CC=mpicc FC=mpif90 CXX=mpicxx". It configured okay, but showed error when compiling the code with "MAKE".
Next, I configured with "CC=icc FC=ifort CXX=icpc", and it worked just fine.

More specific information is as follows.

---

~$ module list

Currently Loaded Modules:

1. TACC-paths 2) Linux 3) cluster-paths 4) intel/15.0.3 5) mvapich2/2.1 6) cluster 7) TACC 8) phdf5/1.8.14

~$ ../configure --prefix=(some_local_dir) --with-hdf5=$TACC_HDF5_BIN/h5pcc CFLAGS="-fPIC" CPPFLAGS="-fPIC" CXXFLAGS="-fPIC" FCFLAGS="-fPIC" LDFLAGS="-L/usr/lib64" CC=mpicc FC=mpif90 CXX=mpicxx
..................long details.............
----------------------------------- SUMMARY -----------------------------------

Package version............... : esio-0.1.9

C++ compiler.................. : mpicxx
C++ compiler flags............ : -fPIC -g -Wno-unknown-pragmas
C compiler.................... : mpicc
C compiler flags.............. : -fPIC -g -traceback -Wall -std=gnu99 -Wcheck -Wpointer-arith -wd424 -wd981 -Wno-unknown-pragmas
Fortran compiler ............. : mpif90
Fortran compiler flags........ : -fPIC -g -warn all -traceback
Install dir................... : /home/01545/pro0104/SOFTWARE/ESIO-0.1.9
HDF CPP flags................. :
HDF C flags................. :
HDF LDFLAGS flags............. :
Build user.................... : pro0104
Build host.................... : login1.wrangler.tacc.utexas.edu
Configure date................ : 2017-08-15 14:40
Build architecture............ : x86_64-unknown-linux-gnu
SVN revision number........... :

---

~$ make
..............long compilation lines..............................
libtool: link: mpif90 -I.. -I../.. -I../esio -fPIC -g -warn all -traceback -Wl,--as-needed -o .libs/concepts2 concepts2.o -Wl,-rpath -Wl,/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib -L/usr/lib64 ../esio/.libs/libesiof.so -L/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib /opt/apps/intel15/mvapich2/2.1/lib/libmpifort.so -L/usr/lib64/ -L/lib /opt/apps/intel15/mvapich2/2.1/lib/libmpi.so -lxml2 -libmad -libumad -libverbs -lrt /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libhdf5_hl.so /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libhdf5.so /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libsz.so -lz -ldl -lm -Wl,-rpath -Wl,/home/01545/pro0104/SOFTWARE/ESIO-0.1.9/lib -Wl,-rpath -Wl,/opt/apps/intel15/mvapich2/2.1/lib -Wl,-rpath -Wl,/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib
ld: cannot find -libverbs
make[3]: *** [concepts2] Error 1
make[3]: Leaving directory /home/01545/pro0104/SOFTWARE/esio-0.1.9/build/examples' make[2]: *** [all] Error 2 make[2]: Leaving directory /home/01545/pro0104/SOFTWARE/esio-0.1.9/build/examples'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/01545/pro0104/SOFTWARE/esio-0.1.9/build'
make: *** [all] Error 2

---

[RhysU]

What happens if you feed it h5pcc and the like for CC, CXX, etc.?

[RhysU]

Any news on attempting to force h5pcc as mentioned above?

[M-K-Lee]

Rhys, I am in the conference. I will test it when I get back to Austin. MK

…

On Tue, Aug 22, 2017 at 2:33 AM, Rhys Ulerich ***@***.***> wrote: Any news on attempting to force h5pcc as mentioned above? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANoMpupLr0Vd3IN_QKqWIFVkBOIS4YgBks5saiHtgaJpZM4O4BTx> .

-- Best regards, MyoungKyu(M.K.) Lee

[M-K-Lee]

Rhys, FYI, Damon generously agreed to work on the issue. (Thank you damon.) Best, MK On Tue, Aug 22, 2017 at 7:46 AM, Myoungkyu Lee <leemyoungkyu@gmail.com> wrote:

…

Rhys, I am in the conference. I will test it when I get back to Austin. MK On Tue, Aug 22, 2017 at 2:33 AM, Rhys Ulerich ***@***.***> wrote: > Any news on attempting to force h5pcc as mentioned above? > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#5 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ANoMpupLr0Vd3IN_QKqWIFVkBOIS4YgBks5saiHtgaJpZM4O4BTx> > . > -- Best regards, MyoungKyu(M.K.) Lee

-- Best regards, MyoungKyu(M.K.) Lee

[nicholasmalaya]

So this ticket can be closed, right?

[dmcdougall]

$ ../configure --prefix=$HOME/esio CFLAGS="-fPIC" CPPFLAGS="-fPIC" CXXFLAGS="-fPIC" FCFLAGS="-fPIC" CC=h5pcc FC=h5pfc CXX=mpicxx && make

... make coffee ...

libtool: link: mpicc -O3 -fPIC -fPIC -g -traceback -Wall -std=gnu99 -Wcheck -Wpointer-arith -wd424 -wd981 -Wno-unknown-pragmas -Wl,--as-needed -o .libs/concepts1 concepts1.o -Wl,-rpath -Wl,/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib  ../esio/.libs/libesio.so -L/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libhdf5_hl.so /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libhdf5.so /opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib/libsz.so -lz -ldl -lm -Wl,-rpath -Wl,/home/02664/damon/esio/lib -Wl,-rpath -Wl,/opt/apps/intel15/mvapich2_2_1/phdf5/1.8.14/x86_64/lib
concepts1.o: In function `main':
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:13: undefined reference to `esio_handle_initialize'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:14: undefined reference to `esio_file_create'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:16: undefined reference to `esio_string_set'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:19: undefined reference to `esio_attribute_write_int'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:22: undefined reference to `esio_line_establish'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:23: undefined reference to `esio_line_write_double'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:25: undefined reference to `esio_file_close'
/home/02664/damon/src/ESIO-release-0.1.9/build/examples/../../examples/concepts1.c:26: undefined reference to `esio_handle_finalize'

Couldn't find a C++ equivalent for h5pcc or h5pfc.

[dmcdougall]

Also getting inconsistencies in whether or not -fPIC is used.

[RhysU]

Have a machine where I can try it out personally? IIRC shared hdf5 Fortran was a trick. - Rhys

…

On Sep 4, 2017 2:52 PM, "Damon McDougall" ***@***.***> wrote: Also getting inconsistencies in whether or not -fPIC is used. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFNq21tkGkMqjz3pVgNCjxhxKWoIoNLks5sfEbmgaJpZM4O4BTx> .

[dmcdougall]

Not sure. I'll see if I can get a recreate on an ICES machine; do you still have access to any of those?

[RhysU]

I doubt it. Let me see what I can recreate on my machine and then we can compare notes. - Rhys

…

On Sep 4, 2017 3:36 PM, "Damon McDougall" ***@***.***> wrote: Not sure. I'll see if I can get a recreate on an ICES machine; do you still have access to any of those? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFNq2TyaNc36rtPPpofbgulRxt2Ds3tks5sfFEfgaJpZM4O4BTx> .

[dmcdougall]

Alright. Let me know what I can try from my end; I realise you most certainly don't have access to Intel's compilers and whatnot.

[RhysU]

How does something like the following treat you on branch develop?

$ cd $HOME/Build
$ wget https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.19.tar.bz2
$ tar xjvf hdf5-1.8.19.tar.bz2
$ cd hdf5-1.8.19
$ ./configure --prefix=$HOME/Stow/hdf5-1.8.19 --enable-parallel --enable-shared
$ make -j
$ make install
$ cd ..
$ export PATH=$HOME/Stow/hdf5-1.8.19/bin:$PATH
$ git clone https://github.com/RhysU/ESIO.git esio
$ cd esio
$ git checkout develop
$ ./bootstrap
$ cd ../
$ mkdir esio-gcc
$ cd esio-gcc
$ ../esio/configure --prefix=$HOME/Stow/esio-0.1.9
$ make -j
$ make check

I unhacked some stupid youthful hackery in b5d3e1c. Notice neither Fortran nor C++ HDF5 wrappers required.

FWIW, on Ubuntu 17.04 couldn't use default HDF5 per #4. I also see a stack smashing complaint come back on one Fortran test case, which is new to me, but is wayyyyyy down in OpenMPI.

[dmcdougall]

That ninja comment edit confused me. I'll let you know shortly.

[dmcdougall]

Compiled successfully. I also tried setting CC=mpicc and the like and that also compiled successfully. Running make check now.

[dmcdougall]

I'm seeing a nontrivial number of test failures. Here's one of them:

login1.wrangler(16)$ cat tests/basic.sh.log
mpiexec -np 1 ./basic
success_code ...................................................... PASS
file_create_and_open ..............................................HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0:
  #000: H5F.c line 522 in H5Fcreate(): unable to create file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 990 in H5F_open(): unable to open file: time = Wed Sep  6 13:55:49 2017
, name = './test.basic.c.1A0tsj', tent_flags = 13
    major: File accessibilty
    minor: Unable to open file
  #002: H5FD.c line 992 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: H5FDmpio.c line 1061 in H5FD_mpio_open(): MPI_File_open failed
    major: Internal error (too specific to document in detail)
    minor: Some MPI function failed
  #004: H5FDmpio.c line 1061 in H5FD_mpio_open(): File does not exist, error stack:
ADIO_RESOLVEFILETYPE_FNCALL(473): Invalid file name ./test.basic.c.1A0tsj
    major: Internal error (too specific to document in detail)
    minor: MPI Error String
esio: ../../esio/esio.c:506: ERROR: Unable to create file
Default esio error handler invoked.
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 80664 RUNNING AT login1.wrangler.tacc.utexas.edu
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================