FAQ
Over time, we have discovered a few problems that many users experience. The solutions to these common problems are posted here.
Use the search feature to find the best answer! Your question might be answered on another page.
Couldn't find an answer here or via search? Check our support options.
Connection Questions
Why does MobaXTerm throw Authorisation not recognized error when I try to log into Palmetto?
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.
Why do I see the notice REMOTE HOST IDENTIFICATION HAS CHANGED when connecting to Palmetto?
REMOTE HOST IDENTIFICATION HAS CHANGED when connecting to Palmetto?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)
Compute Questions
How do I perform a fine-grained check for resource availability?
The following answer applies to Palmetto 1 and the PBS job scheduler. For Palmetto 2, see our main documentation.
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 ~]$
Why does my program crash on login node with the message Killed?
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 (salloc), and
then run the application/command.
Storage Questions
How do I check how much of my /project storage allocation I am currently using?
/project storage allocation I am currently using?There is a command you can use on the login nodes to check your quota usage.
For more details, please see the Indigo quota usage instructions
Why does my folder not show up when I do ls /project or ls /scratch?
ls /project or ls /scratch?We recently introduced an autofs system that automatically mounts the user
directory when it is accessed, 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
/project or /scratch, 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 /project/tiger/football
cd /scratch/tiger
After you access it, you will see it when you do ls /project or ls /scratch.
If there is no read or write activity on the directory for 5 minutes, it will be
unmounted, so next time you will have to cd into it again in order to see it.
Why are my home or scratch directories are sluggish/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, you can use /local_scratch. Unlike /home or the
/scratch directories, which are shared by all nodes, each node has its own
/local_scratch directory. It is much faster to read/write data to
/local_scratch, and doing so will not affect other users. For an example, see
the
local scratch documentation.
However, note that /local_scratch is purged immediately when the job ends, so
you must copy your final data back to /scratch or /home at the end of your
job to avoid data loss.
Why can't I access /software?
/software?Typically losing access to /software means you have an Active Directory
lockout on your account. You should call the
CCIT helpdesk or drop by the
support center in the library so they can
help remove the lock and troubleshoot why it existed. A common cause is having a
device with wrong credentials attempting to authenticate repeatedly on eduroam.
Once the lockout is removed you should have access to /software within an
hour. If you still don't have access, please reach out to us and we
can force sync the storage system.
Open OnDemand Questions
Why can't I request a bigger node or more than 8 hours?
Open OnDemand sessions provide an easy interactive experience for running various workloads for development and testing. We want to ensure users have fast access to resources so their jobs launch faster. We noticed a trend of increased wait times over earlier semesters. When investigating this trend, we discovered many interactive jobs started on Open OnDemand requested large walltimes and were not stopped after computation was complete. These idle jobs tied up compute resources that could have been better utilized by other jobs. We expect this problem to be exacerbated as we remove old CPU nodes and transition nodes to Slurm. The resource limits were put in place to encourage appropriate use of interactive jobs on Open OnDemand. This should enable faster access to resources for everyone.
This decision was also informed by examining interactive queueing policies at national HPC centers ( NERSC: Perlmutter, PSC: Bridges-2, etc.).
Node owners can make full use of their purchased resources and are not limited
to 8 hours. Be sure to change the selected queue from work1 to your owner's
queue at the top of the OnDemand form. Once changing to an owner queue, you
should be able to specify custom chunk count, CPU count, memory, and walltime.
For users who need more resources or runtime, run your code as a batch job. Python scripts, Jupyter notebooks, and R scripts can all be run from a batch job. Within a batch job, you are no longer subjected to the limits shown in the Open OnDemand session creation forms, the limits are higher. Be sure to monitor your job and make reasonable resource requests. We are happy to help you create batch jobs; join us in office hours or submit a support request.
Why are 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 environments with
source activate.
module load anaconda3
source activate <name_of_environment>
Why did my Open OnDemand job fail to launch or quit early?
View the Troubleshooting Guide for OnDemand jobs. Use the link next to the job in OnDemand (if applicable) to submit a ticket if the troubleshooting does not fix the problem.
Other
How do I fix the error undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b (PBS only)?
undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b (PBS only)?The following answer applies to Palmetto 1 and the PBS job scheduler. 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.
Error when creating conda environment after loading anaconda module
If error occurs, please try the following command:
export LD_PRELOAD=""
402: Could not map pixel buffer object
Try running with VirtualGL. Make sure you
specify a device to vglrun, either egl to use the
EGL back end or :0.0 or :0.1 if you
need to use the GLX back end.