`input-mesh` fails to compile on queenbee2 #1119

wwlwpd · 2023-05-05T17:27:13Z

make -j 1 NETCDFPATH=/work/asgs/asgs-prod/opt NETCDF=enable NETCDF4=enable NETCDF4_COMPRESSION=enable MACHINE_NAME=queenbee compiler=intel
ifort -fpp -DINTEL -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/work/asgs/asgs-prod/opt/include -L/work/asgs/asgs-prod/opt/lib -c ../../../output/logging.f90 -lnetcdff
ifort -fpp -DINTEL -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/work/asgs/asgs-prod/opt/include -L/work/asgs/asgs-prod/opt/lib -c ../../../output/adcmesh.f90 -lnetcdff
ifort -fpp -DINTEL -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/work/asgs/asgs-prod/opt/include -L/work/asgs/asgs-prod/opt/lib -c ../nodalattr/nodalattr.f90 -lnetcdff
ifort -fpp -DINTEL -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/work/asgs/asgs-prod/opt/include -L/work/asgs/asgs-prod/opt/lib -c ../../../output/asgsio.f90 -lnetcdff
ifort -fpp -DINTEL -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/work/asgs/asgs-prod/opt/include -L/work/asgs/asgs-prod/opt/lib -o boundaryFinder.x boundaryFinder.f90 adcmesh.o asgsio.o logging.o -lnetcdff
asgsio.o: In function `asgsio_mp_determinenetcdffilecharacteristics_':
asgsio.f90:(.text+0x4d2a): undefined reference to `nodalattr_mp_initnodalattributenames_'
asgsio.f90:(.text+0x4df4): undefined reference to `nodalattr_mp_nodalattributenames_'
asgsio.f90:(.text+0x51f1): undefined reference to `nodalattr_mp_nodalattributenames_'
make: *** [boundaryFinder] Error 1
command for "Step for in util/input/mesh" exited with an error code of 2, stopping. Please fix and rerun.

The text was updated successfully, but these errors were encountered:

wwlwpd · 2023-05-05T17:43:52Z

Basic approach to troubleshoot is:

build with ./install-asgs.sh -b -x "--skip-steps input-mesh"
get into the shell, ./asgsh
start by reproducing the build error by running the failed command,

…linking on QB. Issue 1119: Added explicitly the required libraries during the linking phase, seems everything was correct except this final step. It's a mystery why this was only being exposed on queenbee2 (LONI), but this changes fixes it. Resolves #1119.

…linking on QB. Issue 1119: Added explicitly the required libraries during the linking phase, seems everything was correct except this final step. It's a mystery why this was only being exposed on queenbee2 (LONI), but this changes fixes it. Resolves #1119. Resolves #1121 (PR).

…linking on QB. Issue 1119: Added explicitly the required libraries during the linking phase, seems everything was correct except this final step. It's a mystery why this was only being exposed on queenbee2 (LONI), but this changes fixes it. Resolves #1119. Resolves #1121 (PR). (cherry picked from commit 7b0b5d6) Signed-off-by: wwlwpd <46434714+wwlwpd@users.noreply.github.com>

wwlwpd · 2023-08-11T15:37:13Z

I just tried to login to hatteras, and I don't think my login works any more. Here's how I debug everything.

Given,

prompt> ./init-asgs.sh -b -x "--list-steps"
           setup-env - Updates current environment with variables needed for subsequent steps. It only affects the environment within the asgs-brew.pl environment.
             openmpi - Downloads and builds OpenMPI on all platforms for ASGS. Note: gfortran is required, so any compiler option causes this step to be skipped.
                hdf5 - Downloads and builds the version of HDF5 that has been tested to work on all platforms for ASGS.
             netcdf4 - Downloads and builds the versions of NetCDF and NetCFD-Fortran that have been tested to work on all platforms for ASGS.
              wgrib2 - Downloads and builds wgrib2 on all platforms for ASGS. Note: gfortran is required, so any compiler option passed is overridden.
       cpra-postproc - Runs the makefile and builds associated utilities in the output/cpra_postproc directory
              output - Runs the makefile and builds associated utilities in the output/ directory.
                util - Runs the makefile and builds all associated utilities in the util/ directory.
          input-mesh - Runs the makefile and builds all associated util/input/mesh in the input-mesh/ directory.
     input-nodalattr - Runs the makefile and builds associated utilities in the util/input/nodalattr directory.
                perl - Install local Perl version used for ASGS.
        perl-modules - Install Perl modules used for ASGS.
        image-magick - Install local ImageMagick tools and Perl module Image::Magick.
             python3 - install python 3 locally and install required modules
              ffmpeg - Install ffmpeg and required libraries (nasm)
             gnuplot - Install gnuplot (commandline only)
               units - Install GNU Units utility
                 nco - Install The netCDF Operators (NCO) Toolkit
                pigz - Install pigz, unpigz - parallel gzip
              adcirc - Builds ADCIRC and SWAN if $HOME/adcirc-cg exists.

You can straight up skip breaking steps for debugging purposes. For example,

./init-asgs.sh -x "--skip-steps input-mesh"

You can skip multiple steps, via:

./init-asgs.sh -x "--skip-steps input-mesh,image-magick,..."

This is how I debug. Basically I skip whatever is breaking, then the given command build; then you can run ./asgsh and manually debug the "build" commands present in ./cloud/general/asgs-brew.pl inside of the proper environment.

Also, look at the created ./update-asgs script - it contains the full asgs-brew.pl, which lets you then run it instead of ./init-asgs.sh,

./update-asgs "flags passed to asgs-brew.pl command ..."

wwlwpd · 2023-08-11T15:39:56Z

An extreme command to immediately get to the shell, with nothing built but the environment set up would be:

prompt> ./init-asgs.sh -b -x "--update-shell"
...
prompt> ./asgsh

notstarboard · 2023-08-11T20:34:41Z

All the debugging tips are very useful. It turns out that the issue I was hitting when I ran with --force and the other TMPDIR was actually before the perl creation step, so I may have closed the other issue too early! At any rate, I'm now hitting a similar error message to the above even without the updated TMPDIR and the --force flag, so it is something I'll also have to deal with. Maybe --force works by uninstalling and reinstalling everything and something that it tried to reinstall failed? Unsure. Here's the error I'm hitting:

Writing wrapper ASGSH Shell command wrapper 'update-asgs' for use later...
/usr/share/Modules/software/compiled_w_intel/mvapich2/2.3.7/bin/mpif90

make -j 1 NETCDFPATH=/home/joshua_p/asgs/opt NETCDF=enable NETCDF4=enable NETCDF4_COMPRESSION=enable MACHINE_NAME=hatteras compiler=intel
ifort -cpp -shared-intel -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I../output -I. -I/home/joshua_p/asgs/opt/include -L../output -L/home/joshua_p/asgs/opt/lib -o makeMax.x makeMax.f90 ../output/adcmesh.o ../output/asgsio.o ../output/logging.o -L/home/joshua_p/asgs/opt/lib -lnetcdff
../output/asgsio.o: In function `asgsio_mp_determinenetcdffilecharacteristics_':
asgsio.f90:(.text+0x4e20): undefined reference to `nodalattr_mp_initnodalattributenames_'
asgsio.f90:(.text+0x4eea): undefined reference to `nodalattr_mp_nodalattributenames_'
asgsio.f90:(.text+0x52fc): undefined reference to `nodalattr_mp_nodalattributenames_'
make: *** [makeMax] Error 1
command for "Step for in util/" exited with an error code of 2, stopping. Please fix and rerun.

At any rate, when I run with "--skip-steps util,perl-modules" I'm able to get past both errors (the one like #766 and this one); the full install isn't done yet, but it's been chugging along for another 10+ minutes thus far. I'm going to try to debug more later from within ASGSH as you suggested.

notstarboard · 2023-08-13T21:49:18Z

I feel like I should be able to figure these out, but so far it's just been a lot of unsuccessful trial and error. I'm attaching the output I'm getting from running these commands individually from within ASGSH in the hope that you may have thoughts.

For util, I submitted the following command, and received the output in the attached make_util.txt.

make -j 1 NETCDFPATH=/home/joshua_p/asgs NETCDF=enable NETCDF4=enable NETCDF4_COMPRESSION=enable MACHINE_NAME=hatteras compiler=intel

The error looks like it's having trouble finding the NetCDF module, and the "NETCDFPATH := /usr" here feels sketchy, but given the lines below it it could be just fine; I just don't know what we actually need to include.

For perl-modules, I submitted the following command, and received the output in the attached perl-modules.txt.

bash ./cloud/general/init-perl-modules.sh /home/joshua_p/asgs/perl5

Its output specifically references a build.log file which should have more details on the failure, and I've also attached this. Per build.log, it looks like the build processed errored out after the following command:

icc -Ic -I/home/joshua_p/asgs/opt/perl5/perls/perl-5.38.0/lib/5.38.0/x86_64-linux/CORE '-DVERSION="1.31"' '-DXS_VERSION="1.31"' -fPIC -c '-std=gnu99' -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' '-D_FORTIFY_SOURCE=2' -O2 -o lib/Params/Validate/XS.o lib/Params/Validate/XS.c

It looks like this needs to be run from within asgs/opt/perl5/perls/perl-5.38.0/lib/5.38.0 given the lib paths near the end of the command, but when I try this from the shell I get:

icc: error #10236: File not found:  'lib/Params/Validate/XS.c'
icc: command line error: no files specified; for help type "icc -help"

And, sure enough, lib/Params only has a single file in it: Check.pm. There isn't even a Validate folder. So, I'm not sure if that should all be created during the compilation process / elsewhere in init-perl-modules.sh, or if I'm running this in the wrong place, or what.

Would appreciate any tips or answers you may have!
build.log
make_util.txt
perl-modules.txt

wwlwpd · 2023-08-14T15:53:02Z

@notstarboard I am closing this issue because it was an already solved one. I know it's a little extra work, but please open this up as either another issue or in the discussions. I will converse with you there and will add my debugging steps to the wiki.

wwlwpd · 2023-08-14T16:03:28Z

Troubleshooting steps outlined above:

#1179

wwlwpd changed the title ~~wgrid2 fails to compile on queenbee2~~ input-mesh fails to compile on queenbee2 May 5, 2023

wwlwpd mentioned this issue May 6, 2023

Adding explictly nodalattr.o and nodalattr.mod allows for successful … #1121

Closed

wwlwpd self-assigned this May 6, 2023

wwlwpd closed this as completed in 19fef6c May 8, 2023

notstarboard mentioned this issue Aug 11, 2023

perl install error on new platform #766

Closed

wwlwpd reopened this Aug 11, 2023

wwlwpd closed this as completed Aug 14, 2023

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`input-mesh` fails to compile on queenbee2 #1119

`input-mesh` fails to compile on queenbee2 #1119

wwlwpd commented May 5, 2023

wwlwpd commented May 5, 2023

wwlwpd commented Aug 11, 2023 •

edited

wwlwpd commented Aug 11, 2023

notstarboard commented Aug 11, 2023 •

edited

notstarboard commented Aug 13, 2023

wwlwpd commented Aug 14, 2023 •

edited

wwlwpd commented Aug 14, 2023

input-mesh fails to compile on queenbee2 #1119

input-mesh fails to compile on queenbee2 #1119

Comments

wwlwpd commented May 5, 2023

wwlwpd commented May 5, 2023

wwlwpd commented Aug 11, 2023 • edited

wwlwpd commented Aug 11, 2023

notstarboard commented Aug 11, 2023 • edited

notstarboard commented Aug 13, 2023

wwlwpd commented Aug 14, 2023 • edited

wwlwpd commented Aug 14, 2023

`input-mesh` fails to compile on queenbee2 #1119

`input-mesh` fails to compile on queenbee2 #1119

wwlwpd commented Aug 11, 2023 •

edited

notstarboard commented Aug 11, 2023 •

edited

wwlwpd commented Aug 14, 2023 •

edited