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-rw-r--r--topics/octopus/maintenance.gmi98
-rw-r--r--topics/octopus/recent-rust.gmi76
2 files changed, 174 insertions, 0 deletions
diff --git a/topics/octopus/maintenance.gmi b/topics/octopus/maintenance.gmi
new file mode 100644
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+++ b/topics/octopus/maintenance.gmi
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+# 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
+```