diff --git a/docs/index.md b/docs/index.md index 8a90b99d..db549a42 100644 --- a/docs/index.md +++ b/docs/index.md @@ -22,4 +22,4 @@ the advanced compute capabilities provided with the cluster. Students, faculty, or staff should register for the workshops in advance via the links below. Please bring your laptop to the workshop. - \ No newline at end of file + diff --git a/docs/portal.md b/docs/portal.md index 770fd70d..317244d4 100644 --- a/docs/portal.md +++ b/docs/portal.md @@ -115,4 +115,3 @@ run modules and code with the Slurm scheduler from an SSH session. selecting the "Upload" button. - You can download files and directories by selecting them and then selecting the "Download" button. - diff --git a/modules/m3/applications/crystal/23/1.0.1-1.lua b/modules/m3/applications/crystal/23/1.0.1-1.lua index 3d509c9d..8c69f21c 100644 --- a/modules/m3/applications/crystal/23/1.0.1-1.lua +++ b/modules/m3/applications/crystal/23/1.0.1-1.lua @@ -3,11 +3,10 @@ whatis("CRYSTAL 23 v1.0.1: Must be member of crystal group. Request access at vi local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join crystal group\n" -local found = required_group("crystal") -local found_new = required_group("hpc-crystal") +local valid_groups = userInGroups("hpc-crystal") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("crystal") diff --git a/modules/m3/applications/crystal/23/1.0.1.lua b/modules/m3/applications/crystal/23/1.0.1.lua index 9fbce199..79b9611f 100644 --- a/modules/m3/applications/crystal/23/1.0.1.lua +++ b/modules/m3/applications/crystal/23/1.0.1.lua @@ -3,11 +3,10 @@ whatis("CRYSTAL 23 v1.0.1: Must be member of crystal group. Request access at vi local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join crystal group\n" -local found = required_group("crystal") -local found_new = required_group("hpc-crystal") +local valid_groups = userInGroups("hpc-crystal") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("crystal") diff --git a/modules/m3/applications/gaussian/g09d.lua b/modules/m3/applications/gaussian/g09d.lua index da6ee68a..132927bd 100644 --- a/modules/m3/applications/gaussian/g09d.lua +++ b/modules/m3/applications/gaussian/g09d.lua @@ -3,11 +3,10 @@ whatis("Gaussian 09 D: Must be member of gaussian group. Request access at help@ local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join gaussian group\n" -local found = required_group("gaussian") -local found_new = required_group("hpc-gaussian") +local valid_groups = userInGroups("hpc-gaussian") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("gaussian") diff --git a/modules/m3/applications/gaussian/g16c/haswell.lua b/modules/m3/applications/gaussian/g16c/haswell.lua index 13912fc6..49fb5dad 100644 --- a/modules/m3/applications/gaussian/g16c/haswell.lua +++ b/modules/m3/applications/gaussian/g16c/haswell.lua @@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join gaussian group\n" -local found = required_group("gaussian") -local found_new = required_group("hpc-gaussian") +local valid_groups = userInGroups("hpc-gaussian") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("gaussian") diff --git a/modules/m3/applications/gaussian/g16c/zen3.lua b/modules/m3/applications/gaussian/g16c/zen3.lua index 455632ba..a199ea76 100644 --- a/modules/m3/applications/gaussian/g16c/zen3.lua +++ b/modules/m3/applications/gaussian/g16c/zen3.lua @@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join gaussian group\n" -local found = required_group("gaussian") -local found_new = required_group("hpc-gaussian") +local valid_groups = userInGroups("hpc-gaussian") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("gaussian") diff --git a/modules/m3/applications/gaussview/6.0.16.lua b/modules/m3/applications/gaussview/6.0.16.lua index 1fedbc6c..42eca1c3 100644 --- a/modules/m3/applications/gaussview/6.0.16.lua +++ b/modules/m3/applications/gaussview/6.0.16.lua @@ -2,11 +2,10 @@ whatis("GaussView") local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join gaussian group\n" -local found = required_group("gaussian") -local found_new = required_group("hpc-gaussian") +local valid_groups = userInGroups("hpc-gaussian") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("gaussview") diff --git a/modules/m3/applications/vasp/5.4.4.lua b/modules/m3/applications/vasp/5.4.4.lua index 644f5b0c..b94fee2a 100644 --- a/modules/m3/applications/vasp/5.4.4.lua +++ b/modules/m3/applications/vasp/5.4.4.lua @@ -3,11 +3,10 @@ whatis("VASP 5.4.4: Must be member of vasp group. Request access at via help@smu local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join vasp group\n" -local found = required_group("vasp") -local found_new = required_group("hpc-vasp") +local valid_groups = userInGroups("hpc-vasp") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("vasp") diff --git a/modules/mp/apps/gaussian/g16c02.lua b/modules/mp/apps/gaussian/g16c02.lua index fe1768a2..cf60415c 100644 --- a/modules/mp/apps/gaussian/g16c02.lua +++ b/modules/mp/apps/gaussian/g16c02.lua @@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he local err_message="To use this module you must be in a particular group\n" .. "Please contact help@smu.edu with HPC in the subject to join gaussian group\n" -local found = required_group("gaussian") -local found_new = required_group("hpc-gaussian") +local valid_groups = userInGroups("hpc-gaussian") -if (not found and not found_new) then - LmodError(err_message) +if (not valid_groups) then + LmodBreak(err_message) end family("gaussian") diff --git a/modules/testing/biostats_r/1.0.0.lua b/modules/testing/biostats_r/1.0.0.lua index 3884eeef..bfade169 100644 --- a/modules/testing/biostats_r/1.0.0.lua +++ b/modules/testing/biostats_r/1.0.0.lua @@ -12,6 +12,7 @@ R -- launches an R terminal Rscript script -- run a script ]]) + whatis("Name: Biostats R") whatis("Version: ml-verse:4.4.1") whatis("Category: R") @@ -21,7 +22,6 @@ family("R") extensions("DEMORT, stacks/2.68, freebayes, trimmonatic/0.39, bwa/0.7.18, pear/0.9.11, fastp/0.24.0, dDocent/2.9.8, fastx-toolkit, fastqc, bowtie2, htseq, star/2.7.11b, sra-tools/3.2.0") - always_load('apptainer') local sif_file = '/hpc/m3/containers/biostats_r/biostats_r_1.0.0.sif'