Hi <@UV41DBFAT>,
I seem to remember a PR or issue...
# modulesm
Matthias De Smet
12/08/2025, 2:32 PMHi @Edmund,
I seem to remember a PR or issue in the modules repo with dynamic mem allocation for bwa.
Could you point me towards there? I can’t seem to find it anymore 😞
✅ 1
Matthias De Smet
12/08/2025, 2:36 PMAh nevermind.. It was just applicable to
BWA_INDEXm
Maxime Garcia
12/08/2025, 3:35 PMbwamem2 also I believe
Maxime Garcia
12/08/2025, 3:35 PM@Anders Sune Pedersen was asking questions about that earlier
a
Anders Sune Pedersen
12/08/2025, 4:29 PMYeah, our HPC didn’t handle this new memory allocation so well.
Anders Sune Pedersen
12/08/2025, 4:30 PMFor the test-profile of Sarek, the
memory { 6.B * fasta.size() } Copy code
#PBS -l mem=238.3kb.<http://command.com|command.com>m
Matthias De Smet
12/08/2025, 4:30 PMThats not good 😮
Matthias De Smet
12/08/2025, 4:31 PMSo it’s the dynamic resource stuff that doesn’t work
a
Anders Sune Pedersen
12/08/2025, 4:31 PMhm - not sure if it is a common problem.
Anders Sune Pedersen
12/08/2025, 4:31 PMI think it triggered
Copy code
Illegal attribute or resource value for Resource_List.memAnders Sune Pedersen
12/08/2025, 4:31 PMfrom the queueing system (PBS)
Anders Sune Pedersen
12/08/2025, 4:32 PMThere is also this thing with our HPC that jobs seems to require at least X GB memory to start. (Don’t know the exact value of X - my colleague says 5GB)
m
Matthias De Smet
12/08/2025, 4:32 PMAh ok, so not a broken language feature
a
Anders Sune Pedersen
12/08/2025, 4:33 PMI solved it in that particular module with this :
Copy code
memory {
def bytes = 6.B * (fasta?.size() ?: 0)
def gb = Math.ceil(bytes.toGiga()) as long
gb = Math.max(5L, gb)
return "${gb} GB"
}e
Edmund
12/10/2025, 4:45 PMPR for the future https://github.com/nf-core/modules/pull/8993/files