Potential compilation issue with gwrite_genarray.fh: No such file or directory about adios

[pnorbert]

gwrite_genarray.fh is missing, so try to regenerate it with gpp.py

<adios_source>/utils/gpp/gpp.py genarray.xml

Norbert

On Thu, Oct 10, 2013 at 4:22 PM, yomagg [email protected] wrote:

Hi,

I am compiling ADIOS (master branch) on Kraken. This is an attempt to
instrument ADIOS with TAU. In general it is not important because the issue
happens with one of the Fortran tests

...
Debug: Compiling with Instrumented Code
Executing> ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -g -finstrument-functions -o genarray-genarray.o
genarray.F90:185:0: fatal error: gwrite_genarray.fh: No such file or directory
compilation terminated.
Error: Compilation Failed
Error: Command(Executable) is -- ftn
Error: Full Command attempted is -- ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -g -finstrument-functions -o genarray-genarray.o
Error: Reverting to a Regular Make

make[4]: *** [all] Error 1
make[3]: *** [genarray-genarray.o] Error 1
make[3]: Leaving directory /nics/d/home/smagg/src/adios/kraken-tau/tests/genarray' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory/nics/d/home/smagg/src/adios/kraken-tau/tests'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/nics/d/home/smagg/src/adios/kraken-tau'
make: *** [all] Error 2

The missing file is likely here. Maybe gwrite_arrays.fh? Or something
similar, but simple change of the file names in genarray.F90 and adding the
location of examples/Fortran/arrays to FFLAGS, doesn't work so it is not
gwrite_arrays.fh file

find . -name "*.fh"./examples/Fortran/global-array/gwrite_temperature.fh
./examples/Fortran/global-array/gread_temperature.fh
./examples/Fortran/global-array-time/gread_restart.fh
./examples/Fortran/global-array-time/gwrite_restart.fh
./examples/Fortran/arrays/gwrite_arrays.fh
./examples/Fortran/arrays/gread_arrays.fh
./examples/Fortran/scalars/gwrite_scalars.fh
./examples/Fortran/scalars/gread_scalars.fh

Here is the trick that doesn't work

ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/src/adios/kraken-tau/examples/Fortran/arrays -g -finstrument-functions -o genarray-genarray.o

/nics/d/home/smagg/src/adios/kraken-tau/examples/Fortran/arrays/gwrite_arrays.fh:3.25:
Included at genarray.F90:187:

            + 8 * (NX) * (NY) &
                     1

Error: Symbol 'nx' at (1) has no IMPLICIT type
/nics/d/home/smagg/src/adios/kraken-tau/examples/Fortran/arrays/gwrite_arrays.fh:3.32:
Included at genarray.F90:187:

            + 8 * (NX) * (NY) &
                            1

Error: Symbol 'ny' at (1) has no IMPLICIT type
/nics/d/home/smagg/src/adios/kraken-tau/examples/Fortran/arrays/gwrite_arrays.fh:9.52:
Included at genarray.F90:187:

call adios_write (adios_handle, "var_int_1Darray", p, adios_err)
1
Error: Symbol 'p' at (1) has no IMPLICIT type
/nics/d/home/smagg/src/adios/kraken-tau/examples/Fortran/arrays/gwrite_arrays.fh:8.55:
Included at genarray.F90:187:

call adios_write (adios_handle, "var_double_2Darray", t, adios_err)
1
Error: Symbol 't' at (1) has no IMPLICIT type

Regards,

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[yomagg]

Thanks Norbert.I have generated the missing files as you suggested, however now I am getting the error that the symbol has no IMPLICIT type. I suppose that the gwrite_genarray.fh might be incorrectly generated missing something. Do you have any suggestions how to progress with this thing? Thanks.

ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -g -finstrument-functions -o genarray-genarray.o
gwrite_genarray.fh:31.53:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xy", int_xy, adios_err)
                                                     1
Error: Symbol 'int_xy' at (1) has no IMPLICIT type
gwrite_genarray.fh:32.55:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xyt", int_xyt, adios_err)
                                                       1
Error: Symbol 'int_xyt' at (1) has no IMPLICIT type
gwrite_genarray.fh:33.55:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xyz", int_xyz, adios_err)
                                                       1
Error: Symbol 'int_xyz' at (1) has no IMPLICIT type
gwrite_genarray.fh:25.53:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_x", offs_x, adios_err)
                                                     1
Error: Symbol 'offs_x' at (1) has no IMPLICIT type
gwrite_genarray.fh:26.53:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_y", offs_y, adios_err)
                                                     1
Error: Symbol 'offs_y' at (1) has no IMPLICIT type
gwrite_genarray.fh:27.53:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_z", offs_z, adios_err)
                                                     1
Error: Symbol 'offs_z' at (1) has no IMPLICIT type
gwrite_genarray.fh:14.29:
    Included at genarray.F90:186:

                + 4 * (size_x) * (size_y) &
                             1
Error: Symbol 'size_x' at (1) has no IMPLICIT type
gwrite_genarray.fh:14.40:
    Included at genarray.F90:186:

                + 4 * (size_x) * (size_y) &
                                        1
Error: Symbol 'size_y' at (1) has no IMPLICIT type
gwrite_genarray.fh:16.51:
    Included at genarray.F90:186:

                + 4 * (size_x) * (size_y) * (size_z)
                                                   1
Error: Symbol 'size_z' at (1) has no IMPLICIT type
gwrite_genarray.fh:18.50:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/X", X, adios_err)
                                                  1
Error: Symbol 'x' at (1) has no IMPLICIT type
gwrite_genarray.fh:19.50:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/Y", Y, adios_err)
                                                  1
Error: Symbol 'y' at (1) has no IMPLICIT type
gwrite_genarray.fh:20.50:
    Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/Z", Z, adios_err)
                                                  1
Error: Symbol 'z' at (1) has no IMPLICIT type
Error: Compilation Failed
Error: Command(Executable) is -- ftn
Error: Full Command attempted is -- ftn    -g -O2 -c  genarray.F90   -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include  -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include    -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include   -g -finstrument-functions   -o genarray-genarray.o
Error: Reverting to a Regular Make


make[4]: *** [all] Error 1
make[3]: *** [genarray-genarray.o] Error 1
make[3]: Leaving directory `/nics/d/home/smagg/src/adios/kraken-tau/tests/genarray'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/nics/d/home/smagg/src/adios/kraken-tau/tests'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/nics/d/home/smagg/src/adios/kraken-tau'
make: *** [all] Error 2

[daboyuka]

Hi,

I don't have specific knowledge of this issue in ADIOS, but I've seen
similar errors with FORTRAN compilers in other contexts that may apply here.

There are syntactic differences between different FORTRAN versions, called
"fixed form" and "free form", and sometimes the compiler cannot correctly
infer which version to use, yielding strange syntax errors. I would guess
in this case that "free form" is correct, since it's newer FORTRAN code. If
this is a GNU compiler, you can try forcing one form or the other with
"-ffree-form" or "-ffixed-form". I believe you can pass these flags to
ADIOS at configure time like so: ./configure FFLAGS="-ffree-form"

Not sure this will solve it for you, but may be worth a try.

• Drew

On Thu, Oct 10, 2013 at 6:54 PM, yomagg [email protected] wrote:

Thanks Norbert.I have generated the missing files as you suggested,
however now I am getting the error that the symbol has no IMPLICIT type. I
suppose that the gwrite_genarray.fh might be incorrectly generated missing
something. Do you have any suggestions how to progress with this thing?
Thanks.

ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/

seastar/mpich2-gnu/46/include -g -finstrument-functions -o genarray-genarray.o
gwrite_genarray.fh:31.53:
Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xy", int_xy, adios_err)
1
Error: Symbol 'int_xy' at (1) has no IMPLICIT type
gwrite_genarray.fh:32.55:
Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xyt", int_xyt, adios_err)
1
Error: Symbol 'int_xyt' at (1) has no IMPLICIT type
gwrite_genarray.fh:33.55:
Included at genarray.F90:186:

call adios_write (adios_handle, "/var/int_xyz", int_xyz, adios_err)
1
Error: Symbol 'int_xyz' at (1) has no IMPLICIT type
gwrite_genarray.fh:25.53:
Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_x", offs_x, adios_err)
1
Error: Symbol 'offs_x' at (1) has no IMPLICIT type
gwrite_genarray.fh:26.53:
Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_y", offs_y, adios_err)
1
Error: Symbol 'offs_y' at (1) has no IMPLICIT type
gwrite_genarray.fh:27.53:
Included at genarray.F90:186:

call adios_write (adios_handle, "/aux/offs_z", offs_z, adios_err)
1
Error: Symbol 'offs_z' at (1) has no IMPLICIT type
gwrite_genarray.fh:14.29:
Included at genarray.F90:186:

            + 4 * (size_x) * (size_y) &
                         1

Error: Symbol 'size_x' at (1) has no IMPLICIT type
gwrite_genarray.fh:14.40:
Included at genarray.F90:186:

            + 4 * (size_x) * (size_y) &
                                    1

Error: Symbol 'size_y' at (1) has no IMPLICIT type
gwrite_genarray.fh:16.51:
Included at genarray.F90:186:

            + 4 * (size_x) * (size_y) * (size_z)
                                               1

Error: Symbol 'size_z' at (1) has no IMPLICIT type
gwrite_genarray.fh:18.50:
Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/X", X, adios_err)
1
Error: Symbol 'x' at (1) has no IMPLICIT type
gwrite_genarray.fh:19.50:
Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/Y", Y, adios_err)
1
Error: Symbol 'y' at (1) has no IMPLICIT type
gwrite_genarray.fh:20.50:
Included at genarray.F90:186:

call adios_write (adios_handle, "/dimensions/Z", Z, adios_err)
1
Error: Symbol 'z' at (1) has no IMPLICIT type
Error: Compilation Failed
Error: Command(Executable) is -- ftn
Error: Full Command attempted is -- ftn -g -O2 -c genarray.F90 -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include -g -finstrument-functions -o genarray-genarray.o
Error: Reverting to a Regular Make

make[4]: *** [all] Error 1
make[3]: *** [genarray-genarray.o] Error 1
make[3]: Leaving directory /nics/d/home/smagg/src/adios/kraken-tau/tests/genarray' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory/nics/d/home/smagg/src/adios/kraken-tau/tests'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/nics/d/home/smagg/src/adios/kraken-tau'
make: *** [all] Error 2

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[yomagg]

Interesting. Since I don't need Fortran at all, I wonder if the final solution would be --disable-fortran for the ./configure. This is really, really strange issue, since on this Tuesday, I compiled the same code but without instrumentation and I didn't have such an issue at all.It just compiled. Very, very weird.

I am trying to compile this with GNU compiler. I ran into a lot of troubles when trying to compile plain ADIOS with the intel compiler, so I assume that with instrumentation it might be even worse.

I have checked both -ffree-form and -ffixed-form in an attempt to compile this single file and I got same result 'no IMPLICIT blah blah'. But I didn't check with ./configure. I will try configure with --disable-fortran

> ftn   -ffixed-form  -g -O2 -c  genarray.F90   -DHAVE_CONFIG_H -I. -I../.. -I../../src -I/nics/d/home/smagg/opt/mxml-2.7/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/nics/d/home/smagg/opt/evpath/kraken/gnu/include -I/opt/cray/lustre-cray_ss_s/default/include  -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include    -I/nics/d/home/smagg/opt/tau/2/include -I/opt/cray/mpt/5.3.5/xt/seastar/mpich2-gnu/46/include   -g -finstrument-functions   -o genarray-genarray.o

Magda

[yomagg]

I have just commented that line, and the compilation proceeds ...

185 !#include "gwrite_genarray.fh"

Same thing with copyarray.F90 with commenting lines 53, and 237 I believe (the lines the include the gread_ or gwrite_)