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QUESTION
Given the following Perl code, how could one get code execution if they control $foo
?
ANSWER
Answered 2021-Apr-29 at 21:11You can take advantage of \c
to eat an inserted escape character.
QUESTION
When using Dask with SGE or PBS clusters I sometimes have workers becoming unresponsive.
These workers are highlighted in red in the dashboard Info section with their "Last seen" number constantly increasing.
I know this can happen if submitted tasks hold the GIL for too long but that's not the case here. I'm talking about workers for which something went wrong (probably unrelated to dask or the task itself).
They will not come back and are not detected as dead either.
The problem is that tasks submitted on these workers (they become unresponsive after receiving a task, maybe when loading the environment) never end and block everything.
Is there a setting allowing to "timeout" or "invalidate" a worker if it was unresponsive for a given time ?
If not, is it possible and what would be the recommended way to manually do this invalidation and dispatch remaining tasks on other workers ?
Thanks in advance for any help regarding this issue.
...ANSWER
Answered 2021-Apr-15 at 14:54If anyone is wondering the same thing, the answer was given in the following topic.
Setting the worker-ttl parameter allows to consider a worker as dead if not seen for a specified amount of time.
QUESTION
So basically I am lately always getting the following Error when I delete a message that my Bot sends. The message is not being used by the Bot anymore, but for some reason, it always crashes after deletion.
...ANSWER
Answered 2021-Mar-20 at 18:52Your problem is that you delete the message twice. The first time you delete it right at the start of the command, the second time in the case: "patrol"
. So I would recommend you to only delete it in the switch/case, because in the default
branch you want to reply to the message. This will be your code then (I just removed one line):
QUESTION
How to build MPICH with gfortran-10, gcc-10 and g++-10?
BackgroundI want to build MPICH with grortran-10 so as to be able to use up to date MPI bindings, but I haven't managed to do so. Trying to install MPICH via apt on Ubuntu always uses gfortran 7.5.0 (same version with gcc and g++), even if I have latest version of gfortran installed. Just for clarity, here is my current MPICH and gfortran configuration (installed via apt) :
...ANSWER
Answered 2021-Jan-17 at 10:30I followed advice VladimirF gave me in the comments, and everthing worked out. This site provided all the necessary guidelines. Only a few minor problems had to be dealth with. Before I could create ./configure
file, I was prompted to install some missing autotools, which was simply done using apt
. Once ./configure
file was ready, I passed in the mostly same configuration that apt
originally installed MPICH with (see the long list original question), with 'FC = gfortran-10' 'CC = gcc-10' 'CXX = g++-10'
replacing 'FC = gfortran' 'CC = gcc' 'CXX = g++'
. Several more prompts had to be dealt with (mostly adding something to configuration or installing missing packages, easily done with Synaptic package manager). After doing all the steps, F08 bindings were succesfully built and work properly. Here is my current MPICH configuration :
QUESTION
I have some Fortran code I would like to paralelize with MPI. Appereantly, recomended way to use MPI (MPICH, in my case) with Fortran is through mpi_f08
module (mpi-forum entry on the matter), but I have trouble making it work, since corresponding mod file is simply not created (unlike mpi.mod
, which works fine, but it's not up to date with Fortran standart). This discussion left me under the impression it's because gfortran can't build the F08 bindings. Below you can see my configuration, both gfortran and mpich have been installed throught apt install on ubuntu and should be up to date. I'm unsure about a few things :
- Is there any way to make the Fortran 2008 MPI syntax work with gfortran? From what I came across, it seems the answer is no, but hopefully someone may know a fix. I'm not too versed in this, so any relavant links or more entry level explanation would be greatly appreciated.
- Could using different compiler help? Intel compiler* maybe? I would rather stick with gfortran if reasonable.
- Maybe consistency with current standart isn't such a big deal. From your experience, would it be better to just go with support through mpi.mod module? What problems could I expect then? My application doesn't have much long term ambition, so falling out of support some time later isn't a big problem if it works properly now.
It seem's to have been problem of using outdated version of gfortran. This reduces my question to how to build MPICH with gfortran-10.
* hence the [intel-fortran] tag, feel free to remove it if you think it redundantJust for clarity, there's my gfortran and mpich configuration
...ANSWER
Answered 2021-Jan-16 at 14:57MPICH requires the Fortran compiler to support the array descriptor of Technical Specification 29113, and this is only supported in recent versions of gfortran
(GNU 10 is ok).
Intel compilers have been fine for a while fwiw.
Note that Open MPI is not that picky w.r.t. TS 29113 and does not need support for the array descriptor. GNU 7.5 can be used to generate the mpi_f08
module.
Bottom line, you have two options w.r.t. the mpi_f08
Fortran module:
- use a Fortran support that meets MPICH expectation w.r.t. TS 29113 (e.g. GNU 10, or Intel compilers for example)
- move to Open MPI
QUESTION
Mysql version is 6.7+
Example of the column I need to get a value from below.
json_extract(goal_templates.template_data, group_concat('$.resources'))
->This results in a NULL return for all rows.
{"Resolve housing issues": {"tasks": [{"name": "Use Decision Map to explore paths to resolving'' housing issue", "end_date": "15 days", "taskType": 3, "help_text": "", "resources": [], "start_date": "today", "actionOrder": "1", "recur_every": "", "resource_reference_id": ""}, {"name": "Select a local Debt & Credit Counseling Service", "end_date": "15 days", "taskType": 3, "help_text": "Add & tag local Credit & Debt Counseling Service (Organization)", "resources": ["14579", "14580"], "start_date": "today", "actionOrder": "2", "recur_every": "", "resource_reference_id": "14579, 14580"}, {"name": "[Schedule Credit & Debt Counseling as SGE or RGE]", "end_date": "15 days", "taskType": 3, "help_text": "", "resources": [], "start_date": "today", "actionOrder": "3", "recur_every": "", "resource_reference_id": ""}, {"name": "Rate resource for benefit of those who follow", "end_date": "15 days", "taskType": 3, "help_text": "", "resources": [], "start_date": "today", "actionOrder": "4", "recur_every": "", "resource_reference_id": ""}], "sequence_num": "1"}}
...ANSWER
Answered 2020-Dec-31 at 20:35mysql> select json_extract(template_data, '$."Resolve housing issues".tasks[*].resources') as resources from goal_templates;
+----------------------------------+
| resources |
+----------------------------------+
| [[], ["14579", "14580"], [], []] |
+----------------------------------+
QUESTION
for a sientific projet I need to use the singularity project here : https://github.com/Dfam-consortium/TETools
I manage to run it by running the Wrapper script : bash dfam-tetools.sh
then I get a new environment :
...ANSWER
Answered 2020-Dec-02 at 12:51Edit
Since it is necessary to have access to another directory not in the current one, the singularity command should be run instead of the dfam-tetools.sh
script:
QUESTION
We have switched to using slurm from sge for our cluster job queuing system. In sge when you used the qstat
function it printed the number of cpus/slots in use per job - is there a simple way to do this in slurm? squeue
only shows the number of nodes used per job. Thanks.
ANSWER
Answered 2020-Nov-20 at 13:12The squeue
command has two parameters that allow choosing the columns displayed in the output --format
and --Format
. Each have an option (respectively %c
and NumCPUs
) to display the number of cores requested by the job.
Try with
QUESTION
I am trying to build dssp (https://github.com/cmbi/dssp) on a server-node (not on server-login), and I am facing a problem with how the system finds dependencies. I am working on a centos 7.
The procedure of building dssp is : run ./autogen
to get a configure.sh
file and then execute that one. Then run make
.
Running whereis perl
and whereis perl5
I get:
ANSWER
Answered 2020-Oct-16 at 07:50You have two builds of perl
installed.
/usr/bin/perl
, v5.16.3[1]/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl
, v5.30.0[2]
I shall dub them "system perl
" and "modular perl
" respectively.
- The system
perl
doesn't have Data::Dumper installed.[3] - The modular
perl
does have Data::Dumper installed.[4]
whereis
shows only the system perl
in your PATH, but later commands show perl
invoking the modular perl
. So either perl
is an alias for the modular perl
,[5] or you ran your tests in different environments (i.e. your PATH changed).
Is it appropriate to set PERL5LIB
?
At one point, you set env var PERL5LIB
to /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0
. This is not appropriate.
This is incorrect for the system perl
.[6]
This is unnecessary for the modular perl
. It is redundant.[7]
Why doesn't the system perl
have Data::Dumper installed?
Perl has certain modules that come with it. For virtually as long as support for modules has existed in Perl, this has included Data::Dumper. Data::Dumper should always be available.
However, certain linux distros split Perl into multiple packages. It appears that Data::Dumper is found in the perl(Data::Dumper)
package in CentOS 7.
So the solution is to install that package.
Since Data::Dumper is dual-lived, it can also be installed from CPAN. This doesn't require any special permissions. That said, I usually recommend installing perl
locally instead of messing with the system perl
. It seems you already have such a Perl. This leads us to the next sub-answer.
What if I want to use the modular perl
?
I'm not sure.
A quick experiment leads me to believe this can be solved by simply placing the modular perl
in the PATH before /usr/bin
.
QUESTION
I am working remotely on a server that uses modules to handle dependencies. I am trying to install dssp (https://github.com/cmbi/dssp) . On github one can see the dependencies.
The modules I have loaded are:
...ANSWER
Answered 2020-Sep-15 at 18:30I guess the error is
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