Hi, I have a user that uses QIIME2 on a cluster with the BeeGFS file system. He gets errors that may be related BeeGFS's problems with handling of hard-links. The underlying problem seems to be with nodejs, but I am not certain that QIIME2 itself does not also use hard-links. I have looked at the QIIME2 scripts, but I have not been able to identify the actual line of code that produces error messages. However, the latest version of QIIME2, QIIME2-2023.7.0-foss-2022a.eb, depends upon R-4.2.1-foss-2022a.eb, which in turn depends upon the outdated nodejs-16.15.1-GCCcore-11.3.0.eb. This is what I get, when I try to use nodejs:
On BeeGFS: $ cat /etc/system-release Rocky Linux release 9.1 (Blue Onyx) $ module --quiet purge $ module load nodejs/18.12.1-GCCcore-12.2.0 $ rm -rf ~/.npm $ npm install npm@latest npm ERR! code FETCH_ERROR npm ERR! errno FETCH_ERROR npm ERR! invalid json response body at https://registry.npmjs.org/npm reason: Invalid response body while trying to fetch https://registry.npmjs.org/npm: EPERM: operation not permitted, link '/cluster/home/hna/.npm/_cacache/tmp/3d3f6954' -> '/cluster/home/hna/.npm/_cacache/content-v2/sha512/dc/ea/d3525b62623e8175ff0846eadb788003d59f47a9b6fa5bd7254fc5469ff541980e4e7c34632ac1ca5f8d2cd595f5927ee15ab194afb83f675328b03764b8' $ module --quiet purge $ module load nodejs/18.17.1-GCCcore-12.3.0 $ rm -rf ~/.npm $ npm install npm@latest up to date, audited 219 packages in 3s On Lustre: $ cat /etc/system-release Rocky Linux release 9.2 (Blue Onyx) $ module --quiet purge $ module load nodejs/18.12.1-GCCcore-12.2.0 $ rm -rf ~/.npm $ npm install npm@latest npm WARN EBADENGINE Unsupported engine { npm WARN EBADENGINE package: '[email protected]', npm WARN EBADENGINE required: { node: '^18.17.0 || >=20.5.0' }, npm WARN EBADENGINE current: { node: 'v18.12.1', npm: '8.19.2' } npm WARN EBADENGINE } up to date, audited 219 packages in 2s $ module --quiet purge $ module load nodejs/18.17.1-GCCcore-12.3.0 $ rm -rf ~/.npm $ npm install npm@latest up to date, audited 219 packages in 2s Best regards, Henrik
