Hi, thanks for the reply.
The @anaconda tag in the output just means that attr was installed with the CentOS installer Anaconda (https://en.wikipedia.org/wiki/Anaconda_(installer)) I agree that the issue is similar to the link that you provided. With the exception that here it is EasyBuild who is modifying the LD_LIBRARY_PATH. The build log file has many entries describing that it adds all the dependencies of BigDFT to the LD_LIBRARY_PATH variable, e.g. "INFO Environment variable LD_LIBRARY_PATH set to ...". When the attr path is added it can't perform any normal commands. I confirm this with: $ ls [works] $ export LD_LIBRARY_PATH=/home/scratch3/stly/modules/skylake-modules-test/software/attr/2.5.1-GCCcore-11.2.0/lib:$LD_LIBRARY_PATH $ ls ls: relocation error: /lib64/libacl.so.1: symbol getxattr, version ATTR_1.0 not defined in file libattr.so.1 with link time reference The folder added to LD_LIBRARY_PATH is the one I got from the Easybuild output log. I am unsure on how to proceed. Best regards, Steen [https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Anaconda_Installer_on_Fedora_37.png/1200px-Anaconda_Installer_on_Fedora_37.png]<https://en.wikipedia.org/wiki/Anaconda_(installer)> Anaconda (installer) - Wikipedia<https://en.wikipedia.org/wiki/Anaconda_(installer)> en.wikipedia.org ________________________________ From: Alan O'Cais <[email protected]> Sent: Friday, August 11, 2023 17:57 To: [email protected] <[email protected]>; Steen Lysgaard <[email protected]> Cc: easybuild <[email protected]> Subject: Re: [easybuild] BigDFT build issue: BigDFT-1.9.1-foss-2021b.eb That installation of attr seems to come from conda, I'd probably drop out of the conda environment to do the installation...if that is possible. This issue looks similar and that's what they did: https://stackoverflow.com/questions/74078492/relocation-error-after-export-ld-library-path On 11 August 2023 17:33:17 CEST, Steen Lysgaard <[email protected]> wrote: Hi Alan, adding -ffree-line-length-512 as you suggested makes the build work! Many thanks. One additional question though: On a different server we have the attr package installed by the package manager: $ yum list 'attr*' Installed Packages attr.x86_64 2.4.46-13.el7 @anaconda BigDFT has the attr v. 2.5.1 package as a dependency. Thus when building BigDFT it uses attr v. 2.5.1 and this makes it not recognize any commands e.g. tar. The error message is: List of modules to be treated: I: unknown keys defined in configuration file: addpath tar: relocation error: /lib64/libacl.so.1: symbol getxattr, version ATTR_1.0 not defined in file libattr.so.1 with link time reference jhbuild build: failed to unpack /home/scratch3/stly/modules/skylake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigdft-suite-1.9.1/yaml-0.1.6.tar.gz Commenting out the attr dependency in the easyconfig file leads to a undefined reference errors: D_potrf_double: error: undefined reference to 'dpotrf_' /home/scratch3/stly/modules/skylake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigdft-suite-1.9.1/bigdft_builddir/install/lib/libfutile-1.a(linalg.o):linalg.f90:function __wrapper_linalg_MO D_potrf_simple: error: undefined reference to 'spotrf_' collect2: error: ld returned 1 exit status make[3]: *** [chess_toolbox] Error 1 Any advice on this issue? Best regards, Steen ________________________________ From: Alan O'Cais Sent: Thursday, August 10, 2023 17:09 To: Steen Lysgaard Cc: easybuild Subject: Re: [easybuild] BigDFT build issue: BigDFT-1.9.1-foss-2021b.eb If the below works, can you let us know and I can PR an update the easyconfig. On 10-Aug-23 4:09 PM, Alan O'Cais wrote: Dear Steen, It _looks_ like this could be resolved with giving the option `-ffree-line-length-512` to GFortran. I suspect that __FILE__ is a very long string and it is pushing the line length over the limit (which is why others may not have seen it). The second error is (I think) a consequence of the truncation. Edit the relevant easyconfig line to be local_extra_flags = '-fallow-argument-mismatch -ffree-line-length-512' Alan On 10-Aug-23 3:41 PM, Steen Lysgaard wrote: Hello, I am trying to install BigDFT with the easyconfig file BigDFT-1.9.1-foss-2021b.eb (eb BigDFT-1.9.1-foss-2021b.eb -r --detect-loaded-modules=unload) However, the installation fails, with what seems to be an error with the compilation of a Fortran file of libAbinit which is included in the BigDFT package. The following error message is present in the log file: mpifort -DHAVE_LIBPAW_BIGDFT -DHAVE_DFT_LIBXC -DHAVE_MPI -DHAVE_MPI1 -I. [... Removed Include instructions ...] -O2 -ftree-vectorize -march=native -fno-math-errno -fallow-argument-mismatch -fallow-argument-mismatch -std=legacy -c -o m_libpaw_tools.o `test -f 'libpaw/m_libpaw_tools.F90' || echo '/home/scratch3/stly/modules/icelake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigd ft-suite-1.9.1/libABINIT/src/'`libpaw/m_libpaw_tools.F90 /home/scratch3/stly/modules/icelake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigdft-suite-1.9.1/libABINIT/src/libpaw/m_libpaw_tools.F90:408:132: 408 | & __FILE__,__LINE__) | 1 Error: Line truncated at (1) [-Werror=line-truncation] /home/scratch3/stly/modules/icelake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigdft-suite-1.9.1/libABINIT/src/libpaw/m_libpaw_tools.F90:408:5: 408 | & __FILE__,__LINE__) | 1 Error: Unterminated character constant beginning at (1) f951: some warnings being treated as errors make[1]: *** [Makefile:1908: m_libpaw_tools.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory '/home/scratch3/stly/modules/icelake-modules-test/build/BigDFT/1.9.1/foss-2021b/bigdft-suite-1.9.1/bigdft_builddir/libABINIT/src' make: *** [Makefile:367: all-recursive] Error 1 *** Building libABINIT *** [8/11]^O make -j 113 *** Error during phase build of libABINIT: ########## Error running make -j 113 *** [8/11]^O I can get around the first error with -Wno-error=line-truncation, but not the second one, and I don't really understand it. I have tried the newer 1.9.4 version of BigDFT, where the problem seems to persist. It also happens with foss-2022a Some info: $ uname -r 4.18.0-477.15.1.el8_8.x86_64 $ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: AlmaLinux Description: AlmaLinux release 8.8 (Sapphire Caracal) Release: 8.8 Codename: SapphireCaracal If anybody can help it would be much appreciated. Best regards, Steen [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Steen Lysgaard Scientific Software Developer DTU Energy Mob. +45 51 94 48 86 [email protected]<mailto:[email protected]> Anker Engelunds Vej Building 301 2800 Kgs. Lyngby www.dtu.dk/english<https://www.dtu.dk/english>
