Common problems/issues
Jupyter Notebooks launched through Open Ondemand are asking for a password
This is caused by the "conda initialize" statements in your .bashrc file. Remove the following section from your .bashrc file:
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/software/spackages/linux-rocky8-x86_64/gcc-9.5.0/anaconda3-2022.05-zyrazrj6uvrtukupqzhaslr63w7hj6in/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/software/spackages/linux-rocky8-x86_64/gcc-9.5.0/anaconda3-2022.05-zyrazrj6uvrtukupqzhaslr63w7hj6in/etc/profile.d/conda.sh" ]; then
. "/software/spackages/linux-rocky8-x86_64/gcc-9.5.0/anaconda3-2022.05-zyrazrj6uvrtukupqzhaslr63w7hj6in/etc/profile.d/conda.sh"
else
export PATH="/software/spackages/linux-rocky8-x86_64/gcc-9.5.0/anaconda3-2022.05-zyrazrj6uvrtukupqzhaslr63w7hj6in/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
After this section is removed, activate your conda environemts are with source activate.
module load anaconda3/2022.05-gcc/9.5.0
source activate <name_of_environment>
I get the error "undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b"
This error is caused by a version mismatch between the OpenSSL that is part of the Rocky operating system, and the versions that are required by some software packages. If you get that error, please load these modules:
module load libssh/0.8.5-gcc/9.5.0 krb5/1.19.3-gcc/9.5.0
If that fails, load the anaconda3/2022.05-gcc/9.5.0 module.
Fine-grained checking of resource availability
Up until recently, whatsfree has been the standard tool to identify available computing resources on Palmetto. However, with the additional of compute nodes with large number of cores, large amount of memory, and multiple GPUs card, we have seen instances of nodes using only a portion of the available cores/memory/GPU but are still regarded as unavailable with whatsfree.
To address this issue and improve utilization on Palmetto, a new tool called freeres
(abbreviation of free resources) has been made available. This tool provides a more fine-grained view
into individual nodes of a specific phase. For example, at 15:12 November 19, 2021, whastfree shows
that there are no available nodes on phases 18b, 18c, and 19a:
[lngo@login001 ~]$ whatsfree
C2 CLUSTER (newest nodes with interconnect=HDR except for phase19b)
PHASE 18b TOTAL = 65 FREE = 0 OFFLINE = 0 TYPE = Dell R740 Intel Xeon 6148G, 40 cores, 372GB, HDR, 25ge, V100
PHASE 18c TOTAL = 10 FREE = 0 OFFLINE = 0 TYPE = Dell R740 Intel Xeon 6148G, 40 cores, 748GB, HDR, 25ge, V100
PHASE 19a TOTAL = 28 FREE = 0 OFFLINE = 0 TYPE = Dell R740 Intel Xeon 6248G, 40 cores, 372GB, HDR, 25ge, V100
PHASE 19b TOTAL = 4 FREE = 1 OFFLINE = 0 TYPE = HPE XL170 Intel Xeon 6252G, 48 cores, 372GB, 10ge
PHASE 20 TOTAL = 22 FREE = 0 OFFLINE = 0 TYPE = Dell R740 Intel Xeon 6238R, 56 cores, 372GB, HDR, 25ge, V100S
However, freeres shows that there are many nodes with significant number of cores/memory available on these phases:
[lngo@login001 ~]$ freeres phase18b phase18c phase19a
group file = /software/caci/cluster/phase18b
group file = /software/caci/cluster/phase18c
group file = /software/caci/cluster/phase19a
CPU | GPU | Memory (GB) |
Node Avail Used Free | Avail Used Free | Avail Used Free | State
---------------------------------------------------------------------------
node0060 40 12 28 2 2 0 376 372 4 free
node0152 40 26 14 2 2 0 376 173 203 free
node0064 40 12 28 2 2 0 376 372 4 free
node0084 40 8 32 2 2 0 376 372 4 free
node0059 40 30 10 2 2 0 376 173 203 free
node0096 40 32 8 2 2 0 376 184 192 free
node1302 40 3 37 2 0 2 376 372 4 free
node0123 40 8 32 2 2 0 376 372 4 free
node1228 40 8 32 2 2 0 376 372 4 free
node0146 40 8 32 2 2 0 376 372 4 free
node0131 40 8 32 2 2 0 376 372 4 free
node0148 40 37 3 2 2 0 376 304 72 free
node0156 40 8 32 2 2 0 376 372 4 free
node0181 40 33 7 2 2 0 376 358 18 free
node1523 40 8 32 2 2 0 376 372 4 free
node0209 40 32 8 2 2 0 376 258 118 free
node0201 40 12 28 2 2 0 376 372 4 free
node0045 40 36 4 2 2 0 754 240 514 free
node0176 40 30 10 2 2 0 376 244 132 free
node0246 40 12 28 2 2 0 376 372 4 free
node0183 40 8 32 2 2 0 376 372 4 free
node0153 40 32 8 2 2 0 754 270 484 free
node0766 40 8 32 2 2 0 376 372 4 free
node0219 40 8 32 2 2 0 376 372 4 free
node1266 40 8 32 2 2 0 376 372 4 free
node0032 40 8 32 2 2 0 376 44 332 free
node1397 40 32 8 2 2 0 376 264 112 free
node0047 40 16 24 2 2 0 376 372 4 free
node1415 40 36 4 2 1 1 376 270 106 free
node1438 40 8 32 2 2 0 376 372 4 free
node1459 40 26 14 2 2 0 376 174 202 free
node1462 40 8 32 2 2 0 376 372 4 free
node0079 40 32 8 2 2 0 376 128 248 free
node1414 40 8 32 2 2 0 376 372 4 free
node0089 40 8 32 2 2 0 376 372 4 free
node0136 40 8 32 2 2 0 376 372 4 free
node1521 40 32 8 2 1 1 376 214 162 free
node0020 40 8 32 2 2 0 376 372 4 free
node0040 40 8 32 2 2 0 376 372 4 free
node0058 40 8 32 2 2 0 376 372 4 free
node0137 40 32 8 2 2 0 376 128 248 free
node0119 40 8 32 2 2 0 376 372 4 free
node0130 40 8 32 2 2 0 376 372 4 free
checked 103 nodes in 0.42 Seconds
Taking advantage of freeres, it is possible to request portion of nodes that fit into these available resources.
For example, the following qsub that specifies interconnect=25ge (to imply the usage of these nodes) is allocated in
less than a minute.
[lngo@login001 ~]$ qsub -I -l select=6:ncpus=12:mem=160gb:interconnect=25ge
qsub (Warning): Interactive jobs will be treated as not rerunnable
qsub: waiting for job 4049542.pbs02 to start
qsub: job 4049542.pbs02 ready
[lngo@node0152 ~]$
I bought storage on Palmetto; how do I check how much of it I am currently using?
When you buy Palmetto storage, this storage is automatically backed up every day, and the storage space that you have bought is used to store the back-up snapshots. It is very important that your owned storage is less than 90% full, otherwise backups won't work. To check how much space you are using on your bought storage, you can run the script called checkzfs from the login node. Let's say I bought 22 Tb of storage, and it's called mydata. To check it, I run
checkzfs mydata
The output will look something like this:
DATE: 2021-11-19 14:11:17.878949
============================================
USAGE FOR /zfs/mydata
Purchased: 22.0 TiB
Used: 4.7 TiB
Available: 17.3 TiB
Please leave 10% of the purchased amount for snapshots.
I can see that my storage uses 4.7 Tb out of 22 Tb, so I am good for now. I need to do it from time to time, to make sure my storage does not exceed 90% (in my case, 19.8 Tb). If it does, checkzfs will give me a warning.
MobaXTerm throws Authorisation not recognized error when I try to log into Palmetto
This error looks like this:
/usr/bin/xauth: error in locking authority file /home/username/.Xauthority
MoTTY X11 proxy: Authorisation not recognized
Usually this happens when your home directory is full. Log into Palmetto with another terminal application (for example, PuTTY) and free up some space in your home directory. Then, MobaXTerm should work fine.
I don't see my folder when I do ls /zfs
We recently introduced autofs feature that automatically mounts the user directory to /zfs file system when they access it, and unmounts it after 5 minutes of inactivity. This feature increases the robustness of our file system, and will greatly decrease the visual clutter (especially important if you are accessing Palmetto through a graphical interface). Due to the automatic mounting, you will not initially see your folder in /zfs, and tab completion won't work. However, the folder is still there. You can cd directly into it, and you will not have any issues:
$ cd /zfs/mygroup
After you access it, you will see it when you do ls /zfs. If you won't use it for 5 minutes or longer, it will be unmounted, so next time you will have to cd into it in order to see it.
Program crashes on login node with message Killed
When running commands or editing files on the login node, users may
notice that their processes end abruptly with the error message Killed.
Processes with names such as a.out, matlab, etc.,
are automatically killed on the login node because they may consume
excessive computational resources. Unfortunately, this also means that
benign processes, such as editing a file with the word matlab as part
of its name could also be killed.
Solution: Request an interactive session on a compute node (qsub -I),
and then run the application/command.
Home or scratch directories are sluggish or unresponsive
The /home and /scratch directories can become slow/unresponsive
when a user (or several users) read/write large amounts of data to
these directories. When this happens, all users are affected as these
filesystems are shared by all nodes of the cluster.
To avoid this issue, keep in mind the following:
-
Never use the
/homedirectory as the working directory for jobs that read/write data. If too many jobs read/write data to the/homedirectory, it can render the cluster unusable by all users. Copy any input data to one of the/scratchdirectories and use that/scratchdirectory as the working directory for jobs. Periodically move important data back to the/homedirectory. -
Try to use
/local_scratchwhenever possible. Unlike/homeor the/scratchdirectories, which are shared by all nodes, each node has its own/local_scratchdirectory. It is much faster to read/write data to/local_scratch, and doing so will not affect other users. (see example [here])(https://www.palmetto.clemson.edu/palmetto/userguide_howto_choose_right_filesystem.html).
For MacOS users, problems with logging into Palmetto from the terminal
If you are a Mac user, and try to ssh into Palmetto from the terminal, you might get this error message:
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
SHA256:Z2WLGvz7vX2t9VPap6ITwS3cBlCafN69FoIm8wmmF6g.
Please contact your system administrator.
Add correct host key in /Users/abcd/.ssh/known_hosts to get rid of this message.
Offending RSA key in /Users/abcd/.ssh/known_hosts:5
RSA host key for login.palmetto.clemson.edu has changed and you have requested strict checking.
Host key verification failed.
This is a common problem, and it's easy to fix. Please find the line "Offending RSA key" in the error message. In the example above, the number of the offending key is 5. This means that we have to remove 5th line from the lists of known SSH hosts so this line could be recreated.
There are several ways to fix the error. The first one is, to type in terminal
sed -i '5d' ~/.ssh/known_hosts
(Please replace the number 5 with the number of the offending RSA key from the error message)
Alternatively, you can type in terminal
perl -pi -e 's/\Q$_// if ($. == 5);' ~/.ssh/known_hosts
(Again, instead of number 5, put the number of the offending RSA key)
Error when creating conda environment after loading anaconda module
If error occurs, please try the following command:
`$ export LD_PRELOAD="" `