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Compiler dependency #5

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M-K-Lee opened this issue Aug 15, 2017 · 21 comments
Open

Compiler dependency #5

M-K-Lee opened this issue Aug 15, 2017 · 21 comments

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@M-K-Lee
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M-K-Lee commented Aug 15, 2017

@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
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RhysU commented Aug 16, 2017

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

@RhysU
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RhysU commented Aug 22, 2017

Any news on attempting to force h5pcc as mentioned above?

@M-K-Lee
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M-K-Lee commented Aug 22, 2017 via email

@M-K-Lee
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M-K-Lee commented Aug 30, 2017 via email

@nicholasmalaya
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So this ticket can be closed, right?

@dmcdougall
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dmcdougall commented Sep 4, 2017 •
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$ ../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
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Also getting inconsistencies in whether or not -fPIC is used.

@RhysU
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RhysU commented Sep 4, 2017 via email

@dmcdougall
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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
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RhysU commented Sep 4, 2017 via email

@dmcdougall
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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
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RhysU commented Sep 6, 2017 •
edited
Loading

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

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

@dmcdougall
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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
===================================================================================

@dmcdougall
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dmcdougall commented Sep 6, 2017 •
edited
Loading

find .. -iname "test.basic.c.1A0tsj" doesn't return anything, so this file is missing.

Edit: I'm in a build directory, one level below the repo root.

@RhysU
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RhysU commented Sep 10, 2017

Unable to create file looks fishy-- can you manually run a test or two? They're driven from bash scripts underneath the tests/ directory.

@dmcdougall
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Same thing:

c252-135.wrangler(83)$ pwd
/home/02664/damon/git/ESIO/build/tests
c252-135.wrangler(84)$ ibrun ./basic  # For this case, this is basically mpiexec -np 1
TACC: Starting up job 52033
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
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 = Mon Sep 11 17:13:59 2017
, name = '/tmp/test.basic.c.SWcAXO', 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 /tmp/test.basic.c.SWcAXO
    major: Internal error (too specific to document in detail)
    minor: MPI Error String
esio: ../../esio/esio.c:507: ERROR: Unable to create file
Default esio error handler invoked.
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[c252-135.wrangler.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid: 24417) exited with status 1
TACC: MPI job exited with code: 1

TACC: Shutdown complete. Exiting.

Making a directory called foo and setting ESIO_TEST_OUTPUT_DIR=foo yields the same error message.

I also can't gdb the test binary:

c252-135.wrangler(85)$ ../libtool --mode=execute gdb --tui ./basic

(gdb) start
Temporary breakpoint 1 at 0x406e55: file ../../tests/basic.c, line 64.
Starting program: /home/02664/damon/git/ESIO/build/tests/.libs/basic
Cannot create process: No such process
During startup program exited with code 127.

Line 64 of basic.c is the FCT_BGN() macro, and I have no idea what that is doing.

To preserve my sanity, I'm writing a small C program that creates an HDF5 file "in parallel". The quotes mean that, simply, this is a one-process MPI code.

@dmcdougall
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To preserve my sanity, I'm writing a small C program that creates an HDF5 file "in parallel". The quotes mean that, simply, this is a one-process MPI code.

My hello world H5Fcreate in parallel doesn't work, so this is a problem on Wrangler, not with ESIO.

@RhysU
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RhysU commented Sep 12, 2017

Just /tmp not writeable either from the shell or inside an mpiexec? Does tweaking TMPDIR to, say, $HOME/tmp change anything?

@dmcdougall
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It's filesystem-independent; I'm pretty sure the phdf5 install on Wrangler is just borked.

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4 participants
@RhysU @dmcdougall @nicholasmalaya @M-K-Lee