search

Unidata / netcdf-fortran

Official GitHub repository for netCDF-Fortran libraries, which depend on the netCDF C library. Install the netCDF C library first.
Other
244 stars 98 forks source link

Failure to build netcdf fortran 4.6.0 w/ netcdf-c 4.9.2 on Centos 7 #406

Open HathewayWill opened 1 year ago

HathewayWill commented 1 year ago

@edhartnett

Environment:

Centos 7 - VM Libraries:L zlib - 1.2.13 hdf5 - 1.14.1.2 netcdf-c - 4.9.0 (pass) 4.9.2 (fail) netcdf-fortran - 4.6.0 libpng - 1.6.39 mpich - 4.1.2 jasper - 1.900.1 pnetcdf - 1.12.3

see test scripts and log files attached in zip folder:

Errors.zip

WardF commented 1 year ago

Thanks for providing the error logs! From the failed log, I see the following: 

opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /home/workhorse/WRF_SFIRE/Libs/NETCDF/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): warning: relocation against `H5T_STD_U16LE_g' in read-only section `.text'
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /home/workhorse/WRF_SFIRE/Libs/NETCDF/lib/libnetcdf.a(libdispatch_la-dinstance.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: final link failed: bad value

Long story short, you'll need to reinstall libnetcdf (netcdf-c); when you do so, specify CFLAGS='-fPIC' (in addition to any other CFLAGS you're setting). It appears that you're setting that when configuring netCDF-fortran. Can you see what happens if you recompile libnetcdf with CFLAGS=-fPIC, or let me know that you're already doing so?

HathewayWill commented 1 year ago

Already doing so.

CFLAGS = -O3 -fPIC -fPIE

On Wed, Jul 26, 2023, 6:20 PM Ward Fisher @.***> wrote:

Thanks for providing the error logs! From the failed log, I see the following:

opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /home/workhorse/WRF_SFIRE/Libs/NETCDF/lib/libnetcdf.a(libnchdf5_la-nc4hdf.o): warning: relocation against H5T_STD_U16LE_g' in read-only section.text' /opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: /home/workhorse/WRF_SFIRE/Libs/NETCDF/lib/libnetcdf.a(libdispatch_la-dinstance.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC /opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/ld: final link failed: bad value

Long story short, you'll need to reinstall libnetcdf (netcdf-c); when you do so, specify CFLAGS='-fPIC' (in addition to any other CFLAGS you're setting). It appears that you're setting that when configuring netCDF-fortran. Can you see what happens if you recompile libnetcdf with CFLAGS=-fPIC, or let me know that you're already doing so?

— Reply to this email directly, view it on GitHub https://github.com/Unidata/netcdf-fortran/issues/406#issuecomment-1652673354, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4FUT5RRV3PKEN2GEXPAQQDXSGQ33ANCNFSM6AAAAAA2XXP4UI . You are receiving this because you authored the thread.Message ID: @.***>

HathewayWill commented 1 year ago

@WardF

The shell script attached in the zip files should show the exact steps I took for recreation.

HathewayWill commented 1 year ago

@WardF

So for some reason CFLAGS is either getting removed or over written from autotools maybe?

WardF commented 1 year ago

@HathewayWill I'm revisiting this and the shell scripts you've provided; I am not immediately certain why CFLAGS is being removed. How are you invoking the script, simply running it from the command line vis-a-vis:

$ ./netcdf-4.9.2.sh

Or is it being invoked some other way?

HathewayWill commented 1 year ago

@WardF being built from source tar file.

HathewayWill commented 12 months ago

@WardF @edwardhartnett

This issue also occurs on any ubuntu system less than 22.04.2

Something about netcdf 4.9.1 & 4.9.2 w/ 4.6.1 causes the CFLAGS to be removed.

WardF commented 11 months ago

That is interesting; CFLAGS is an environmental variable, and I'm unable to replicate the issue where the CFLAGS just disappear. When you invoke the script, are you running it directly, are you running it via sudo or su?

HathewayWill commented 11 months ago

That is interesting; CFLAGS is an environmental variable, and I'm unable to replicate the issue where the CFLAGS just disappear. When you invoke the script, are you running it directly, are you running it via sudo or su?

Let me send a file with the installation. @WardF

netcdf_error.zip

this is for ubuntu 20, works fine on ubuntu 22

HathewayWill commented 11 months ago

@WardF

Just wanted to give you an update. I tested netcdf 4.9.0, 4.9.1, 4.9.2 with netcdf fortrtan 4.6.1

and the only one that works is 4.9.0 with 4.6.1. So the error seems to be with netcdf-c.

Tested on these operating systems: MacOS 13, Centos9, Centos7, Ubuntu22, Ubuntu20

WardF commented 10 months ago

@WardF

Just wanted to give you an update. I tested netcdf 4.9.0, 4.9.1, 4.9.2 with netcdf fortrtan 4.6.1

and the only one that works is 4.9.0 with 4.6.1. So the error seems to be with netcdf-c.

Tested on these operating systems: MacOS 13, Centos9, Centos7, Ubuntu22, Ubuntu20

Running the script you provided on a Ubuntu 23.10 machine, I'm seeing a failure although it is unrelated to any changes in CFLAGS; rather, it looks like there is a problem in how the script is trying to build libnetcdf. Investigating, and will follow up; I've added a -e invocation before the compilation step in the script, so that an error will cause the script to stop running.

HathewayWill commented 10 months ago

I havent tried on Ubuntu 23 yet myself. So for all I know it may work on that one.

Unfortunately I'm sick with COVID so I can't access my computer

On Fri, Jan 5, 2024, 12:51 PM Ward Fisher @.***> wrote:

@WardF https://github.com/WardF

Just wanted to give you an update. I tested netcdf 4.9.0, 4.9.1, 4.9.2 with netcdf fortrtan 4.6.1

and the only one that works is 4.9.0 with 4.6.1. So the error seems to be with netcdf-c.

Tested on these operating systems: MacOS 13, Centos9, Centos7, Ubuntu22, Ubuntu20

Running the script you provided on a Ubuntu 23.10 machine, I'm seeing a failure although it is unrelated to any changes in CFLAGS; rather, it looks like there is a problem in how the script is trying to build libnetcdf. Investigating, and will follow up; I've added a -e invocation before the compilation step in the script, so that an error will cause the script to stop running.

— Reply to this email directly, view it on GitHub https://github.com/Unidata/netcdf-fortran/issues/406#issuecomment-1879121211, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4FUT5VWXD3EZIVAFYGTETDYNBDTRAVCNFSM6AAAAAA2XXP4UKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZZGEZDCMRRGE . You are receiving this because you were mentioned.Message ID: @.***>

WardF commented 10 months ago

Take care of yourself, I will keep working on this; I am travelling but have put a pin on this so we can get it sorted out. I'm finding an error in the script provided in which configure for libhdf5 fails, reporting a failure related to -m64 for gfortran. libhdf5 is not generated, which means libnetcdf is not generated, which means netCDF-Fortran will not build. Peculiar. I will stand up an older VM to see if the behavior changes, or if this is something on the latest Ubuntu and not related to the initial issue.

HathewayWill commented 6 months ago

@WardF

What did you need again? I just got back