diff options
Diffstat (limited to 'topics/octopus')
-rw-r--r-- | topics/octopus/maintenance.gmi | 98 | ||||
-rw-r--r-- | topics/octopus/recent-rust.gmi | 76 |
2 files changed, 174 insertions, 0 deletions
diff --git a/topics/octopus/maintenance.gmi b/topics/octopus/maintenance.gmi new file mode 100644 index 0000000..65ea52e --- /dev/null +++ b/topics/octopus/maintenance.gmi @@ -0,0 +1,98 @@ +# Octopus/Tux maintenance + +## To remember + +`fdisk -l` to see disk models +`lsblk -nd` to see mounted disks + +## Status + +octopus02 +- Devices: 2 3.7T SSDs + 2 894.3G SSDs + 2 4.6T HDDs +- **Status: Slurm not OK, LizardFS not OK** +- Notes: + - `octopus02 mfsmount[31909]: can't resolve master hostname and/or portname (octopus01:9421)`, + - **I don't see 2 drives that are physically mounted** + +octopus03 +- Devices: 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK +- Notes: **I don't see 2 drives that are physically mounted** + +octopus04 +- Devices: 4 7.3 T SSDs (Neil) + 1 4.6T HDD + 1 3.7T SSD + 2 894.3G SSDs +- Status: Slurm NO, LizardFS OK (we don't share the HDD) +- Notes: no + +octopus05 +- Devices: 1 7.3 T SSDs (Neil) + 5 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK +- Notes: no + +octopus06 +- Devices: 1 7.3 T SSDs (Neil) + 1 4.6T HDD + 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK (we don't share the HDD) +- Notes: no + +octopus07 +- Devices: 1 7.3 T SSDs (Neil) + 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK +- Notes: **I don't see 1 device that is physically mounted** + +octopus08 +- Devices: 1 7.3 T SSDs (Neil) + 1 4.6T HDD + 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK (we don't share the HDD) +- Notes: no + +octopus09 +- Devices: 1 7.3 T SSDs (Neil) + 1 4.6T HDD + 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK (we don't share the HDD) +- Notes: no + +octopus10 +- Devices: 1 7.3 T SSDs (Neil) + 4 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK (we don't share the HDD) +- Notes: **I don't see 1 device that is physically mounted** + +octopus11 +- Devices: 1 7.3 T SSDs (Neil) + 5 3.7T SSDs + 2 894.3G SSDs +- Status: Slurm OK, LizardFS OK +- Notes: on + +tux05 +- Devices: 1 3.6 NVMe + 1 1.5T NVMe + 1 894.3G NVMe +- Status: Slurm OK, LizardFS OK (we don't share anything) +- Notes: **I don't have a picture to confirm physically mounted devices** + +tux06 +- Devices: 2 3.6 T SSDs (1 from Neil) + 1 1.5T NVMe + 1 894.3G NVMe +- Status: Slurm OK, LizardFS (we don't share anything) +- Notes: + - **Last picture reports 1 7.3 T SSD (Neil) that is missing** + - **Disk /dev/sdc: 3.64 TiB (Samsung SSD 990: free and usable for lizardfs** + - **Disk /dev/sdd: 3.64 TiB (Samsung SSD 990): free and usable for lizardfs** + +tux07 +- Devices: 3 3.6 T SSDs + 1 1.5T NVMe (Neil) + 1 894.3G NVMe +- Status: Slurm OK, LizardFS +- Notes: + - **Disk /dev/sdb: 3.64 TiB (Samsung SSD 990): free and usable for lizardfs** + - **Disk /dev/sdd: 3.64 TiB (Samsung SSD 990): mounted at /mnt/sdb and shared on LIZARDFS: TO CHECK BECAUSE IT HAS NO PARTITIONS** + +tux08 +- Devices: 3 3.6 T SSDs + 1 1.5T NVMe (Neil) + 1 894.3G NVMe +- Status: Slurm OK, LizardFS +- Notes: no + +tux09 +- Devices: 1 3.6 T SSDs + 1 1.5T NVMe + 1 894.3G NVMe +- Status: Slurm OK, LizardFS +- Notes: **I don't see 1 device that is physically mounted** + +## Neil disks +- four 8TB SSDs on the right of octopus04 +- one 8TB SSD in the left slot of octopus05 +- six 8TB SSDs bottom-right slot of octopus06,07,08,09,10,11 +- one 4TB NVMe and one 8TB SSDs on tux06, NVME in the bottom-right of the group of 4 on the left, SSD on the bottom-left of the group of 4 on the right +- one 4TB NVMe on tux07, on the top-left of the group of 4 on the right +- one 4TB NVMe on tux08, on the top-left of the group of 4 on the right diff --git a/topics/octopus/recent-rust.gmi b/topics/octopus/recent-rust.gmi new file mode 100644 index 0000000..7ce8968 --- /dev/null +++ b/topics/octopus/recent-rust.gmi @@ -0,0 +1,76 @@ +# Use a recent Rust on Octopus + + +For impg we currently need a rust that is more recent than what we have in Debian +or Guix. No panic, because Rust has few requirements. + +Install latest rust using the script + +``` +curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh +``` + +Set path + +``` +. ~/.cargo/env +``` + +Update rust + +``` +rustup default stable +``` + +Next update Rust + +``` +octopus01:~/tmp/impg$ . ~/.cargo/env +octopus01:~/tmp/impg$ rustup default stable +info: syncing channel updates for 'stable-x86_64-unknown-linux-gnu' +info: latest update on 2025-05-15, rust version 1.87.0 (17067e9ac 2025-05-09) +info: downloading component 'cargo' +info: downloading component 'clippy' +info: downloading component 'rust-docs' +info: downloading component 'rust-std' +info: downloading component 'rustc' +(...) +``` + +and build the package + +``` +octopus01:~/tmp/impg$ cargo build +``` + +Since we are not in guix we get the local dependencies: + +``` +octopus01:~/tmp/impg$ ldd target/debug/impg + linux-vdso.so.1 (0x00007ffdb266a000) + libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe404001000) + librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe403ff7000) + libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe403fd6000) + libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe403fd1000) + libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe403e11000) + /lib64/ld-linux-x86-64.so.2 (0x00007fe404682000) +``` + +Login on another octopus - say 02 you can run impg from this directory: + +``` +octopus02:~$ ~/tmp/impg/target/debug/impg +Command-line tool for querying overlaps in PAF files + +Usage: impg <COMMAND> + +Commands: + index Create an IMPG index + partition Partition the alignment + query Query overlaps in the alignment + stats Print alignment statistics + +Options: + -h, --help Print help + -V, --version Print version +``` |