Computing Resources: Difference between revisions

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(Imaging for Drug Screening)
(Bioterium IP)
 
(24 intermediate revisions by the same user not shown)
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{| class="wikitable" style="margin:auto"
{| class="wikitable" style="margin:auto"
|+ CPB Storage Requirements
|+ CPB Storage Requirements in TB (terabytes)
|-
|-
! Type of Data !! Project !! Lab !! 2021 || 2022 || 2023 || 2024 || 2025
! Type of Data !! Project !! Lab !! 2021 || 2022 || 2023 || 2024 || 2025
|-
|-
| MRD || Routine || Molecular Biology ||  
| Raw MRD (MiSeq) || Routine || Molecular Biology || style="text-align:right;" | || style="text-align:right;" | || style="text-align:right;" | || style="text-align:right;" | || style="text-align:right;" |
|-
| Processed MRD (Vidjil) || Routine || Molecular Biology || style="text-align:right;" |0.05 || style="text-align:right;" |0.07 || style="text-align:right;" |0.20 || style="text-align:right;" |0.30 || style="text-align:right;" |0.40
|-
|-
| Exome || Precision Medicine || Epigenomics ||  
| Exome || Precision Medicine || Epigenomics ||  
Line 12: Line 14:
| Methylome || Precision Medicine || Epigenomics ||  
| Methylome || Precision Medicine || Epigenomics ||  
|-
|-
| Mass spectra || DESI || Leukemia Biology / Pathology ||  
| Mass spectra || DESI || Leukemia Biology / Pathology || style="text-align:right;" |4 || style="text-align:right;" |- || style="text-align:right;" |- || style="text-align:right;" |- || style="text-align:right;" |-
|-
| Imaging || Drug Screening || Leukemia Biology ||  ||  || style="text-align:right;" |15 || style="text-align:right;" |25 ||
|-
| Panel || Drug Screening || Leukemia Biology ||  ||  ||  || style="text-align:right;" |0.4 ||
|-
| Methylome || Drug Screening || Leukemia Biology ||  ||  ||  || style="text-align:right;" |0.03 ||
|-
| RNASeq || Drug Screening || Leukemia Biology ||  ||  ||  || style="text-align:right;" |0.4 ||
|-
| Methylome || FINEP || All ||  ||  ||  ||  || style="text-align:right;" |0.5
|-
| RNASeq || FINEP || All ||  ||  ||  ||  || style="text-align:right;" |4
|-
| Exome || FINEP || All ||  ||  ||  ||  || style="text-align:right;" |8
|-
| Total || || || style="text-align:right;" |4.05 || style="text-align:right;" |0.07 || style="text-align:right;" |15.2 || style="text-align:right;" |26.3 || style="text-align:right;" |12.9
|-
|}
 
{| class="wikitable" style="margin:auto"
|+ Virtual Machines for Host: Machine 60
|-
! Name !! IP !! RAM (GB) !! Disk (TB) !! Processors
|-
| Vidjil || 200.136.108.242 || 12 || 1.0 || 16
|-
| RNASeq || 10.10.70.114 || 64 || 1.0 || 16
|-
| RStudio || 10.10.70.50 || 65 || 4.0 || 1
|-
| Bioterium || 192.168.200.241 || 12 || 0.1 || 4
|-
| Total || || 224 || 12.0 || 24
|-
|}
 
{| class="wikitable" style="margin:auto"
|+ New Machines Bought in 2024
|-
! Name !! IP !! RAM (GB) !! Disk (TB) !! Cores !! Use
|-
| Node1 || 10.10.70.59 || 256 || 7 || 48 || Migo
|-
|-
| Imaging || Drug Screening || Leukemia Biology || || || 15 || 25 ||
| Node2 || 10.10.70.61 || 256 || 7 || 48 || Drug Screening Dashboards
|-
|-
| Panel || Drug Screening || Leukemia Biology ||  
| Node3 || 10.10.70.62 || 256 || 7 || 48 || Protein 3D Modeling
|-
|-
| Methylome || Drug Screening || Leukemia Biology ||  
| Node4 || 10.10.70.63 || 256 || 7 || 48 || Drug Screening Processing
|-
|-
| RNASeq || Drug Screening || Leukemia Biology ||  
| Tirana || 10.10.70.64 || 128 || 65 || 80 || Genomic analyses
|-
|-
|}
|}
Making entire 7 TB disk available on node1-4:
sudo lvm
lvm> vgs
  VG    #PV #LV #SN Attr  VSize VFree
  fedora  1  1  0 wz--n- 6.98t 6.97t
lvm> lvcreate -L 6.97t fedora
  Rounding up size to full physical extent 6.97 TiB
  Logical volume "lvol0" created.
Quit lvm
sudo mkdir -vp /data
sudo mkfs.ext4 /dev/fedora/lvol0
  mke2fs 1.47.0 (5-Feb-2023)
  Discarding device blocks: done                           
  Creating filesystem with 1870995456 4k blocks and 233877504 inodes
  Filesystem UUID: ac2a59ab-e038-4013-aeb6-bb3889b6720e
  Superblock backups stored on blocks:
    32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
    4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968,
    102400000, 214990848, 512000000, 550731776, 644972544
  Allocating group tables: done                           
  Writing inode tables: done                           
  Creating journal (262144 blocks): done
  Writing superblocks and filesystem accounting information: done
Add the following line to /etc/fstab
  /dev/fedora/lvol0 /data ext4 defaults 0 2
Test with
  sudo mount -a

Latest revision as of 19:38, 17 April 2025

CPB Storage Requirements in TB (terabytes)
Type of Data Project Lab 2021 2022 2023 2024 2025
Raw MRD (MiSeq) Routine Molecular Biology
Processed MRD (Vidjil) Routine Molecular Biology 0.05 0.07 0.20 0.30 0.40
Exome Precision Medicine Epigenomics
ctDNA Circular Tumoral DNA Molecular Biology
Methylome Precision Medicine Epigenomics
Mass spectra DESI Leukemia Biology / Pathology 4 - - - -
Imaging Drug Screening Leukemia Biology 15 25
Panel Drug Screening Leukemia Biology 0.4
Methylome Drug Screening Leukemia Biology 0.03
RNASeq Drug Screening Leukemia Biology 0.4
Methylome FINEP All 0.5
RNASeq FINEP All 4
Exome FINEP All 8
Total 4.05 0.07 15.2 26.3 12.9
Virtual Machines for Host: Machine 60
Name IP RAM (GB) Disk (TB) Processors
Vidjil 200.136.108.242 12 1.0 16
RNASeq 10.10.70.114 64 1.0 16
RStudio 10.10.70.50 65 4.0 1
Bioterium 192.168.200.241 12 0.1 4
Total 224 12.0 24
New Machines Bought in 2024
Name IP RAM (GB) Disk (TB) Cores Use
Node1 10.10.70.59 256 7 48 Migo
Node2 10.10.70.61 256 7 48 Drug Screening Dashboards
Node3 10.10.70.62 256 7 48 Protein 3D Modeling
Node4 10.10.70.63 256 7 48 Drug Screening Processing
Tirana 10.10.70.64 128 65 80 Genomic analyses

Making entire 7 TB disk available on node1-4:

sudo lvm

lvm> vgs 

 VG     #PV #LV #SN Attr   VSize VFree
 fedora   1   1   0 wz--n- 6.98t 6.97t

lvm> lvcreate -L 6.97t fedora 

 Rounding up size to full physical extent 6.97 TiB
 Logical volume "lvol0" created.

Quit lvm

sudo mkdir -vp /data

sudo mkfs.ext4 /dev/fedora/lvol0 

 mke2fs 1.47.0 (5-Feb-2023)
 Discarding device blocks: done                            
 Creating filesystem with 1870995456 4k blocks and 233877504 inodes
 Filesystem UUID: ac2a59ab-e038-4013-aeb6-bb3889b6720e
 Superblock backups stored on blocks: 
   32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 
   4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968, 
   102400000, 214990848, 512000000, 550731776, 644972544
 Allocating group tables: done                            
 Writing inode tables: done                            
 Creating journal (262144 blocks): done
 Writing superblocks and filesystem accounting information: done

Add the following line to /etc/fstab 

 /dev/fedora/lvol0 /data ext4 defaults 0 2

Test with 

 sudo mount -a
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