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Issues while building (pio_nc.c) #2001

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coderodyhpc opened this issue Feb 10, 2025 · 14 comments
Open

Issues while building (pio_nc.c) #2001

coderodyhpc opened this issue Feb 10, 2025 · 14 comments

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@coderodyhpc
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Hello,
I'm trying to compile v2.6.2 but building generates the error:

/home/ubuntu/pio2/src/clib/pio_nc.c: In function ‘PIOc_def_var_fill’:
/home/ubuntu/pio2/src/clib/pio_nc.c:2433:56: error: ‘_FillValue’ undeclared (first use in this function); did you mean ‘NC_FillValue’?
 2433 |                     ierr = nc_put_att(file->fh, varid, _FillValue, xtype, 1, fill_valuep);
      |                                                        ^~~~~~~~~~
      |                                                        NC_FillValue
/home/ubuntu/pio2/src/clib/pio_nc.c:2433:56: note: each undeclared identifier is reported only once for each function it appears in
/home/ubuntu/pio2/src/clib/pio_nc.c: In function ‘PIOc_inq_var_fill’:
/home/ubuntu/pio2/src/clib/pio_nc.c:2577:52: error: ‘_FillValue’ undeclared (first use in this function); did you mean ‘NC_FillValue’?
 2577 |                 ierr = nc_get_att(file->fh, varid, _FillValue, fill_valuep);
      |                                                    ^~~~~~~~~~
      |                                                    NC_FillValue
make[2]: *** [src/clib/CMakeFiles/pioc.dir/build.make:216: src/clib/CMakeFiles/pioc.dir/pio_nc.c.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1259: src/clib/CMakeFiles/pioc.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

I saw #1994 and though that maybe using the branch version might fix the issue, but the error still appears. My only potential explanation (or fix) would be the netCDF version, but I would definitely prefer to not have more than one netCDFs in the system.
Thanks.
P.S.

CC=mpicc FC=mpif90 cmake -DPIO_ENABLE_TIMING=OFF -DNetCDF_C_PATH=/opt/atrium/netcdf -DNetCDF_Fortran_PATH=/opt/atrium/netcdf -DPnetCDF_PATH=/opt/atrium/netcdf /home/ubuntu/pio2

-- # PIO Configuration Summary
==============================

# General
-------
PIO Version:            2.6.2
Configured On:          Mon Feb 10 15:02:41 UTC 2025
Host System:            aarch64-Linux-6.8.0-1021-aws
Build Directory:        /home/ubuntu/pio2
Install Prefix:         /usr/local

# Compiling Options
-----------------
C Compiler:             GNU 11.4.0
CFLAGS:                  -std=gnu99
CPPFLAGS:                -DLINUX -DCPRGNU -I/home/ubuntu/pio2 -I/home/ubuntu/pio2/src/clib -I/home/ubuntu/pio2/src/clib -I/home/ubuntu/pio2/src/clib -I/home/ubuntu/pio2/src/clib/../ncint -I/opt/atrium/netcdf/include -I/opt/atrium/netcdf/include
LDFLAGS:
Shared Library:         no
Static Library:         yes
Extra libraries:

Fortran Compiler:       GNU 11.4.0
FFLAGS:                  -fallow-argument-mismatch
FCFLAGS:
More Fortran Flags:      -DLINUX -DCPRGNU -I/home/ubuntu/pio2 -I/home/ubuntu/pio2/src/flib -I/home/ubuntu/pio2/src/flib -I/opt/atrium/netcdf/include -I/opt/atrium/netcdf/include

# Features
--------
PnetCDF Support:        yes
SZIP Write Support:     no
Parallel Filters:       yes
NetCDF/HDF5 Support:    no
NetCDF/HDF5 Par I/O:    yes
NetCDF Integration:     no
PIO Logging:            no
MPIEXEC:                mpiexec
Fortran:                yes

-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/pio2
@jedwards4b
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The latest version of the netcdf library has changed this, however you can enable legacy symbols by building with NETCDF_ENABLE_LEGACY_MACROS. See

https://github.com/Unidata/netcdf-c/blob/main/include/netcdf.h#L118

@jedwards4b
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Please try with branch github.com:jedwards4b/ParallelIO.git
dc7329f..2a5086e fillvalue_fix.wif -> fillvalue_fix.wif
and let me know if it works.

@coderodyhpc
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I tried recompiling netCDF-c with the flag --enable-unsafe-macros but still got the error while building. Let me try your 2nd suggestion and I will let you know.

@coderodyhpc
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coderodyhpc commented Feb 10, 2025 •
edited
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@jedwards4b. Sorry, I can see your commit (with 10 modified files) but cannot clone the branch (there is a message indicating 'This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.').
P.S. Github indicates that one of the checks is pending, maybe I just need to wait a few minutes).

@jedwards4b
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It is a fork, the repo is https://github.com/jedwards4b/ParallelIO.git
add the remote with
git remote add jpedev https://github.com/briandobbins/ParallelIO.git

@coderodyhpc
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I'm unfamiliar with git remote so I might be doing something wrong (not sure). I tried several combinations such as:

$ git clone https://github.com/jedwards4b/ParallelIO
$ cd ParallelIO
$ git remote add jpedev https://github.com/briandobbins/ParallelIO.git
$ git fetch jpedev 
$ git switch -c jpedev
From https://github.com/briandobbins/ParallelIO
 * [new branch]        add_2GiB_local_contig_data_limit -> jpedev/add_2GiB_local_contig_data_limit
...
 * [new tag]           pio1_7_3                         -> pio1_7_3
Switched to a new branch 'jpedev'

At this point, trying cmake and make results in the same error as earlier (the only very minor difference is that the building breaks at 34% versus 30% as in the original build).

@jedwards4b
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After the git fetch command you should just
checkout the branch with
git checkout fillvalue_fix.wif

@coderodyhpc
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It seems to have gone over that bump but it's now generating the error:

[ 82%] Building Fortran object src/flib/CMakeFiles/piof.dir/pio.F90.o
/home/ubuntu/ParallelIO/src/flib/pio.F90:78:22:

   78 |        PIO_def_var   ,        &
      |                      1
Error: Symbol ‘pio_def_var_zstandard’ referenced at (1) not found in module ‘pio_nf’
/home/ubuntu/ParallelIO/src/flib/pio.F90:88:33:

   88 |        PIO_inq_var_quantize     , &
      |                                 1
Error: Symbol ‘pio_inq_var_filter_ids’ referenced at (1) not found in module ‘pio_nf’
/home/ubuntu/ParallelIO/src/flib/pio.F90:90:33:

   90 |        PIO_inq_var_filter_ids   , &
      |                                 1
Error: Symbol ‘pio_inq_var_filter_info’ referenced at (1) not found in module ‘pio_nf’
/home/ubuntu/ParallelIO/src/flib/pio.F90:91:33:

   91 |        PIO_inq_var_filter_info  , &
      |                                 1
Error: Symbol ‘pio_inq_filter_avail’ referenced at (1) not found in module ‘pio_nf’
/home/ubuntu/ParallelIO/src/flib/pio.F90:92:33:

   92 |        PIO_inq_filter_avail     , &
      |                                 1
Error: Symbol ‘pio_def_var_szip’ referenced at (1) not found in module ‘pio_nf’
make[2]: *** [src/flib/CMakeFiles/piof.dir/build.make:104: src/flib/CMakeFiles/piof.dir/pio.F90.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1350: src/flib/CMakeFiles/piof.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

@jedwards4b
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I'm sorry, this must be why it got lost instead of being merged. I'll have to work on it and get back to you.

@coderodyhpc
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OK.

@jedwards4b
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I'm unable to reproduce your problem. I do have a newer gnu compiler than you are using, but I'm not sure what the difference might be otherwise.

One possible cause might be the hdf5 version on which netcdf was built. I am using hdf5/1.12.3, if you are using a 1.14 version of hdf5 this may be the problem.

# General
-------
PIO Version:		2.6.2
Configured On:		Tue 11 Feb 2025 06:55:30 AM MST
Host System:		x86_64-Linux-5.14.21-150400.24.18-default
Build Directory: 	/glade/u/home/jedwards/sandboxes/ParallelIO/bldn493
Install Prefix:         /usr/local

# Compiling Options
-----------------
C Compiler:		GNU 12.4.0
CFLAGS:			 -std=gnu99  
CPPFLAGS:		 -DLINUX -DCPRGNU -DTIMING -I/glade/u/home/jedwards/sandboxes/ParallelIO/bldn493 -I/glade/u/home/jedwards/sandboxes/ParallelIO/src/clib -I/glade/u/home/jedwards/sandboxes/ParallelIO/bldn493/src/clib -I/glade/u/home/jedwards/sandboxes/ParallelIO/src/clib -I/glade/u/home/jedwards/sandboxes/ParallelIO/src/clib/../ncint -I/glade/u/apps/derecho/24.12/spack/opt/spack/netcdf/4.9.3/gcc/12.4.0/jt7q/include
LDFLAGS:		 
Shared Library:		no
Static Library:		yes
Extra libraries:	

Fortran Compiler:       GNU 12.4.0
FFLAGS:                  -fallow-argument-mismatch
FCFLAGS:                
More Fortran Flags:	 -DLINUX -DCPRGNU -I/glade/u/home/jedwards/sandboxes/ParallelIO/bldn493 -I/glade/u/home/jedwards/sandboxes/ParallelIO/src/flib -I/glade/u/home/jedwards/sandboxes/ParallelIO/bldn493/src/flib -I/glade/u/apps/derecho/24.12/spack/opt/spack/netcdf/4.9.3/gcc/12.4.0/jt7q/include

# Features
--------
PnetCDF Support:	no
SZIP Write Support:	yes
Parallel Filters:	no
NetCDF/HDF5 Support:	no
NetCDF/HDF5 Par I/O:	no
NetCDF Integration:	no
PIO Logging:		no
MPIEXEC:		mpiexec
Fortran:		yes

@coderodyhpc
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Yes, I'm using HDF5 v1.14.5. The compiler is not so new because the OS is still Ubuntu 22.04 (will migrate to Ubuntu 24.04 in the next few days).
P.S. As a temporal solution, I did which I said I wanted to avoid and installed netCDF-c v4.9.2 (compartmentalized in a different directory). Then, PIO built smoothly.

@jedwards4b
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I will have a pio 2.6.5 soon with a port to netcdf v4.9.3. Are you still using hdf5 v1.14.5 with your netcdf v4.9.2 build? Let me know if you have more issues, but the first thing I would suspect is HDF5.

@coderodyhpc
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@jedwards4b, hdf5 v1.14.5, netcdf v4.9.2 and PIO v2.6.2 seem to be working well together, no problem thus far.

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@jedwards4b @coderodyhpc