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--- i:placenta:data [2019/07/22 11:10]
Igor Chernyavsky [DLS registration & data access]
+++ i:placenta:data [2022/03/07 13:23] (current)
Igor Chernyavsky [Running COMSOL]
@@ Line 16: / Line 16: @@
 **[[https://icat.diamond.ac.uk/#/login | DLS Data Archive ]]** (accessing long-term storage for scans older than 40 days; see [[https://www.diamond.ac.uk/Users/Experiment-at-Diamond/IT-User-Guide/Not-at-DLS/Retrieve-data.html|data retrieval]] for more tips).
+[[https://savu.readthedocs.io/en/latest/user_guides/user_training/ | Savu ]] is a preferred Python-based tool for reconstructing raw DLS tomography data (i.e. radiographic projections).
 ==== Setting-up and Connecting ====
@@ Line 29: / Line 29: @@
 From now on, all you need to do is to double-click on the desktop NoMachine link and enter your //Federal User ID// and password. Note that you will need to select (or create a new) //Virtual Desktop//.
+Alternatively, you could connect via ''ssh'' (e.g. to run a download operation remotely: ''wget https...'')
+  $ YourFedID@nx.diamond.ac.uk
 ==== Remote SuRVoS operation ====
 Run the following commands in a Terminal: ''Applications --> System Tools --> Terminal''.
 <code>
-$ module load global/cluster
+$ module load hamilton
-$ qlogin -q high.q@@com14 -l exclusive -l gpu_arch=Pascal -P i13
+$ qlogin -P i13 -l gpu=1 -l gpu_arch=Pascal -l exclusive
 $ module load survos
 $ survos &
@@ Line 47: / Line 49: @@
 List of Compute Nodes: ''qhost''\\
 Other possible graphical options for high GPU / Memory Usage:
-<code>qlogin -q high.q@@com14 -l exclusive -l gpu=1,nvidia_tesla -P i13</code>
+<code>
+module load global/cluster
+qlogin -q high.q@@com14 -l exclusive -l gpu=1,nvidia_tesla -P i13
+</code>
+Similarly, to run Avizo 2019.1 (//on DLS campus only//)
+<code>module load avizo/2019.1; avizo</code>
 Further details are available in the [[http://www.diamond.ac.uk/Beamlines/Mx/I24/I24-Manual/Remote-Access/Connection-to-Diamond/data-processing.html|online beamline manual]].
@@ Line 81: / Line 89: @@
   * **On Linux or MacOS**: open a //Terminal emulator// and run\\
-  ''$ ssh -Y **username**@e-a07maat1101**X**.it.manchester.ac.uk''
+  ''$ ssh -Y **username**@e-a07maat1101<wrap em>X</wrap>.it.manchester.ac.uk''
   * **On Windows**: install and run [[https://www.putty.org|PuTTY]]. Enter ''e-a07maat1101**X**.it.manchester.ac.uk'' as the //Host Name//, SSH as the //Connection Type// and hit [Open].
-Here **username** is your UoM username, and **''X''** is the reference letter ('a' to 'l') from the Table below (if unsure, use **''a''** for CS1 as a starting point).
+Here **username** is your UoM username, and ''<wrap em>X</wrap>'' is the reference letter ('a' to 'l') from the Table below (if unsure, use **''a''** for CS1 as a starting point).
+**Note 1**: If you are using MacOS or Windows, you also need to install and run an ''X Server'' first (see more details on [[https://kb.iu.edu/d/bdnt|X-forwarding]]).
+**Note 2**: On a university-managed Linux PC, you could connect directly via a name alias, e.g. ''$ ssh -Y cs1'' .\\ \\
 ^  Ref (X)  ^ Name ^  Core Count  ^ Core Speed and Type ^  RAM (GiB)  ^ Note ^
@@ Line 92: / Line 105: @@
 |  c        | cs3  |  8   | 3.3 GHz (Intel Xeon E5-2643)   |  128  | |
 |  d        | cs4  |  8   | 3.3 GHz (Intel Xeon E5-2643)   |  128  | |
-|  e        | cs5  |  12  | 2.5 GHz (Inter Xeon E5-2430v2) |  128  | |
+|  e        | cs5  |  12  | 2.5 GHz (Inter Xeon E5-2430v2) |  128  | [offline] |
 |  f        | cs6  |  12  | 2.5 GHz (Intel Xeon E5-2430v2) |  128  | |
 |  g        | cs7  |  12  | 2.5 GHz (Intel Xeon E5-2430v2) |  128  | |
 |  h        | cs8  |  12  | 2.5 GHz (Intel Xeon E5-2430v2) |  128  | |
-|  i        | cs9  |  16  | 3.0 GHz (Intel Xeon E5-2623v3) |  256  | |
+|  i        | cs9  |  8 (x2)  | 3.0 GHz (Intel Xeon E5-2623v3) |  256  | |
-|  j        | cs10 |  16  | 3.0 GHz (Intel Xeon E5-2623v3) |  256  | |
+|  j        | cs10 |  8 (x2)  | 3.0 GHz (Intel Xeon E5-2623v3) |  256  | no COMSOL |
-|  k        | cs11 |  32  | 3.0 GHz (AMD Opteron 6220)     |  256  | CPU-intensive |
+|  k        | cs11 |  12 (x2)  | 3.4 GHz (Intel Xeon 6128)      |  1280  | CPU- & Memory-intensive; no COMSOL |
-|  l        | cs12 |  12  | 2.5 GHz (Intel Xeon E5-2430v2) |  192  | |
+|  l        | cs12 |  12  | 2.5 GHz (Intel Xeon E5-2430v2) |  192  |  |
-|    | citadel |  8 (x2)  | 3.4 GHz (Intel Xeon E5-1680v4) |  128  | GPU-intensive (Nvidia GTX1080 8GB 1.6GHz)  |
+|  m        | cs13 |  56 (x2)  | 2.2 GHz (Intel Xeon 6238R) |  1024  | CPU- & Memory-intensive; 892GB SSD (/tmp) |
+|  n        | cs14 |  56 (x2)  | 2.2 GHz (Intel Xeon 6238R) |  1024  | CPU- & Memory-intensive; 892GB SSD (/tmp) |
+|    | minerva |  20 (x2)  | 2.2 GHz (Intel Xeon 4114) |  1536  | Memory- & GPU-intensive (2x Nvidia P100 16GB); 2 TB HDD |
+|    | citadel |  8 (x2)  | 3.4 GHz (Intel Xeon E5-1680v4) |  256  | Visualisation & GPU-intensive (Nvidia GTX1080 8GB); 8 TB HDD |
-Note that all CS cores run in a single-thread mode (HT is switched off).
+Note that cs1-cs8 cores run in a single-thread mode (HT is switched off).
@@ Line 121: / Line 137: @@
 <code>
-$ module load comsol53
+$ module load COMSOL/5.6 #or COMSOL/6.0
 $ comsol &
 </code>
+**Note 1**: If there are errors related to OpenGL, try
+<code>
+$ comsol -3drend sw &
+</code>
+**Note 2**: COMSOL is //not// available on compute servers ''cs10'' and ''cs11''.
+**Note 3**: You could check available software versions by
+<code>
+$ module avail
+</code>
+To install COMSOL on a self-managed PC or laptop, download the [[https://livemanchesterac-my.sharepoint.com/:u:/g/personal/chris_paul_manchester_ac_uk/EUu_mH4g5TxOj2Zj02jPpdYBN5fD0RfE5BK9lPLB0RzF7Q?e=4%3aD1k4ox&at=9 | distributive [6 GB]]] (multi-platform ISO disk image, supporting Linux, MacOS and Windows) and use the following details during the setup:
+<code>licence port@hostname: 15700@lfarm4.eps.manchester.ac.uk; licence number: 7076735</code>
 ==== Running MATLAB ====
@@ Line 133: / Line 164: @@
+==== Other software ====
-<div rightalign>--- //Igor Chernyavsky, 2019/07/15 18:00// ---</div>
+[[https://manchester.saasiteu.com/Modules/SelfService/#knowledgeBase/view/AFC87036FF584A79ABFABA678D76FBA7
+ | GraphPad Prism 8.0 Installer]] - see instructions.
+[[http://www.itservices.manchester.ac.uk/software/ | UoM Research Software Repository]]
+**Note**: When running your code at the University compute cluster (known as Computational Shared Facility, [[http://ri.itservices.manchester.ac.uk/csf3 | CSF]]), use the following to enable Internet access (e.g. to install necessary packages for Julia, Python, R, etc.):
+<code>
+module load tools/env/proxy
+</code>
+<div rightalign>--- //Igor Chernyavsky, 2021/07/22 15:00// ---</div>
 ===== Mounting misc Remote file systems on Linux =====
+Before you start, make sure there is an empty directory (e.g. ''~/Shared'') in your ''home'' directory that you are going to mount.
   * Mount UoM **RDS-SSH Data Share**
 <code>
-sshfs UoM_USERNAME@rds-ssh.itservices.manchester.ac.uk:/mnt/eps01-rds/Placental-Biophysics-Group/ ~/PDrive/RDS/
+sshfs UoM_USERNAME@rds-ssh.itservices.manchester.ac.uk:/mnt/eps01-rds/Placental-Biophysics-Group/ ~/Shared/RDS/
-fusermount -u ~/PDrive/RDS/
+fusermount -u ~/Shared/RDS/
 </code>
   * Mount UoM **P-Drive**
 <code>
-sudo mount -t cifs -o user=UoM_USERNAME,domain=ds.man.ac.uk,sec=ntlmsspi,uid=`id -u`,gid=`id -g` //nask.man.ac.uk/home$ ~/PDrive/
+sudo mount -t cifs -o user=UoM_USERNAME,domain=ds.man.ac.uk,sec=ntlmsspi,uid=`id -u`,gid=`id -g` //nask.man.ac.uk/home$ ~/Shared/PDrive/
-sudo umount ~/PDrive/
+sudo umount ~/Shared/PDrive/
 </code>
   * Mount **Google Drive** via [[https://github.com/astrada/google-drive-ocamlfuse/|gdfuse]]
 <code>
-google-drive-ocamlfuse ~/PDrive/GDrive/
+google-drive-ocamlfuse ~/Shared/GDrive/
-fusermount -u ~/PDrive/GDrive/
+fusermount -u ~/Shared/GDrive/
 </code>
   * Mount **Dropbox** via [[https://github.com/rianhunter/dbxfs|dbxfs]] (N.B. use '''-o nonempty''' option if sure; you might also need to install the following ''Ubuntu'' packages: ''libfuse2 build-essential libssl-dev libffi-dev python3-pip'')
 <code>
-dbxfs ~/PDrive/Dropbox/
+dbxfs ~/Shared/Dropbox/
-fusermount -u ~/PDrive/Dropbox/
+fusermount -u ~/Shared/Dropbox/
+</code>
+For uploading a large file (>~ 10GB) or multiple files, use [[https://github.com/andreafabrizi/Dropbox-Uploader|dropbox_uploader]] script:
+<code>
+./dropbox_uploader -s -p upload /LOCAL_FOLDER /REMOTE_FOLDER
+</code>
+  * Mount **DLS I13 Data Storage** (only available for **60 days** after the beamtime)
+<code>
+sshfs FedID_USERNAME@nx.diamond.ac.uk:/dls/i13/data/ ~/Shared/DLS/
+fusermount -u ~/Shared/DLS/
 </code>
 <div rightalign>--- //Igor Chernyavsky, 2019/05/24 21:12// ---</div>

i/placenta/data.1563793817.txt.gz · Last modified: 2019/07/22 11:10 by Igor Chernyavsky