# Run HADDOCK2.4 using slurm

**URL:** <https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855>\
**Category:** Uncategorized\
**Created:** [February 21, 2024, 12:23pm UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855 "2024-02-21T12:23:47Z")\
**Posts on this page:** 8\
**Page:** 1

<div class="post-metadata">

**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [February 21, 2024, 12:23pm UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/1 "2024-02-21T12:23:47Z")

</div>

Hi,  
I am using HADDOCK local version 2.4 successfully and now I want to start running HADDCOK using slurm. I read the tutorial online but did not understand it. Is this what I should do?  
This it what I have now:  
in run.cns  
{===\>} queue\_1=“/bin/tcsh”;  
{===\>} cns\_exe\_1=“/home/qnt/drorimi2/software/cns\_solve\_1.3/intel-x86\_64bit-linux/source/cns\_solve-2305211622.exe”;  
{===\>} cpunumber\_1=18;

and in config.local  
set CNSTMP=/home/qnt/drorimi2/software/cns\_solve\_1.3/intel-x86\_64bit-linux/source/cns\_solve-2305211622.exe  
set QUEUETMP=/bin/tcsh  
set NUMJOB=4  
set QUEUESUB=QueueSubmit\_concat.py

Should I change in run.cns to {===\>} queue\_1=“sbatch”;  
My script for slurm is:  
#!/bin/bash

#SBATCH -p prod # Submit to ‘stdmemq’ Partitiion or queue  
#SBATCH -J HADDOCK\_4\_4\_5\_f\_6\_1 # Name the job as ‘MPItest’  
#SBATCH -o MCSA1test-%j.out # Write the standard output to file named ‘jMPItest-\<job\_number\>.out’  
#SBATCH -e MCSA1test-%j.err # Write the standard error to file named ‘jMPItest-\<job\_number\>.err’  
#SBATCH -t 0-10:00:00 # Run for a maximum time of 0 days, 12 hours, 00 mins, 00 secs  
#SBATCH --nodes=1 # Request N nodes  
#SBATCH --ntasks-per-node=18 # Request n cores or task per node  
#SBATCH --mem-per-cpu=1GB # Request 4GB RAM per core

pwd # prints current working directory  
date # prints the date and time

/usr/lib64/mpich/bin/mpirun -np --ntasks-per-node ??? \<run\_HADDOCK\_slurm.sh\> run\_HADDOCK\_slurm.out #run the MPI job

What should I have the executable file be? (instead of ???) and did I change run.cns correctly? is there any other file I should change? Where should I put the code provided in [HADDOCK2.4 manual - Frequently Asked Questions – Bonvin Lab](https://www.bonvinlab.org/software/haddock2.4/faq/#running-haddock-on-a-cluster-using-a-queuing-system-eg-torque-or-slurm)?

Thank you

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [February 21, 2024, 1:15pm UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/2 "2024-02-21T13:15:24Z")

</div>

There are two ways you could run it:

**1) You start haddock2.4 on the master node and let HADDOCK submit individual jobs to the batch system.**

For this you would define in run.cns:

```auto
{===>} queue_1=“sbatch <any options you might want to add>”;
{===>} cns_exe_1=“/home/qnt/drorimi2/software/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2305211622.exe”;
{===>} cpunumber_1=18;

```

Possibly you will need the full path to sbatch. And you could define as many cpus as you are allowed to use.  
The corresponding config file would look like:

```auto
set CNSTMP=/trinity/home/enmr/software/cns/cns_solve_1.31-UU/intel-x86_64bit-linux/bin/cns
set QUEUETMP=“sbatch <any options you might want to add>"
set NUMJOB=50
set QUEUESUB=QueueSubmit_concat.py

```

  

**2) You submit the full HADDOCK process to a node and use X cores on that node.**  
In that scenario you would write a sbatch script that requests one node and X cores, and starts haddock. No MPI! You will first need to call haddock2.4 once to create the rundir and edit the run.cns file. Then submit to the batch system

```auto

#!/bin/bash
#SBATCH -p prod # Submit to ‘stdmemq’ Partitiion or queue
#SBATCH -J HADDOCK_4_4_5_f_6_1 # Name the job
#SBATCH -o MCSA1test-%j.out # Write the standard output to file named ‘jMPItest-<job_number>.out’
#SBATCH -e MCSA1test-%j.err # Write the standard error to file named ‘jMPItest-<job_number>.err’
#SBATCH -t 0-10:00:00 # Run for a maximum time of 0 days, 12 hours, 00 mins, 00 secs
#SBATCH --nodes=1 # Request N nodes
#SBATCH --ntasks-per-node=18 # Request n cores or task per node
#SBATCH --mem-per-cpu=1GB # Request 4GB RAM per core

date # prints the date and time

source <path-to-haddock-installation/haddock_configure.sh

cd <haddock-rundir>

haddock2.4 >haddock.out

```

And in run.cns you would have:

```auto

{===>} queue_1=“/bin/tcsh”;
{===>} cns_exe_1=“/home/qnt/drorimi2/software/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2305211622.exe”;
{===>} cpunumber_1=18;

```

Making sure of course that the path to the executable and the haddock installation are accessible from a node.

Cheers

Alexandre

---

<div class="post-metadata">

**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [February 21, 2024, 1:55pm UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/3 "2024-02-21T13:55:59Z")

</div>

Thank you!  
I am trying the second way  
my batch code looks like this:  
"  
#!/bin/bash

#SBATCH -p prod # Submit to ‘stdmemq’ Partitiion or queue  
#SBATCH -J HADDOCK\_4\_4\_5\_f\_6\_1 # Name the job  
#SBATCH -o MCSA1test-%j.out # Write the standard output to file named ‘jMPItest-\<job\_number\>.out’  
#SBATCH -e MCSA1test-%j.err # Write the standard error to file named ‘jMPItest-\<job\_number\>.err’  
#SBATCH -t 0-10:00:00 # Run for a maximum time of 0 days, 12 hours, 00 mins, 00 secs  
#SBATCH --nodes=1 # Request N nodes  
#SBATCH --ntasks-per-node=18 # Request n cores or task per node  
#SBATCH --mem-per-cpu=1GB # Request 4GB RAM per core

date # prints the date and time  
source /home/qnt/drorimi2/software/haddock2.4-2023-01/haddock\_configure.sh  
cd /home/qnt/drorimi2/full\_analize\_40PDB/7pll/HADDOCK/run\_7pll\_4\_4\_5\_flex\_6\_1  
haddock2.4 \>&haddock.out  
"

And the run.param is just as you wrote (without changing)  
However, this is the error I get:  
"  
which: no naccess in (/home/qnt/drorimi2/anaconda3/envs/haddock2.4/bin:/usr/condabin:/private/chem/qchem/5.4.2r/exe:/private/chem/qchem/5.4.2r/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/opt/intel/mkl/10.2.4.032/lib/em64t:/opt/intel/impi/4.1.0/bin64:/opt/hpmpi/bin:/home/qnt/majort/bin/babel/openbabel-2.2.3/bin:/private/chem/bin:/home/qnt/drorimi2/bin:/home/qnt/drorimi2/bin/wham:/home/qnt/drorimi2/bin/perl:.:/home/qnt/drorimi2/anaconda3/bin)  
which: no pales in (/home/qnt/drorimi2/anaconda3/envs/haddock2.4/bin:/usr/condabin:/private/chem/qchem/5.4.2r/exe:/private/chem/qchem/5.4.2r/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/opt/intel/mkl/10.2.4.032/lib/em64t:/opt/intel/impi/4.1.0/bin64:/opt/hpmpi/bin:/home/qnt/majort/bin/babel/openbabel-2.2.3/bin:/private/chem/bin:/home/qnt/drorimi2/bin:/home/qnt/drorimi2/bin/wham:/home/qnt/drorimi2/bin/perl:.:/home/qnt/drorimi2/anaconda3/bin)  
which: no tensor2 in (/home/qnt/drorimi2/anaconda3/envs/haddock2.4/bin:/usr/condabin:/private/chem/qchem/5.4.2r/exe:/private/chem/qchem/5.4.2r/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/opt/intel/mkl/10.2.4.032/lib/em64t:/opt/intel/impi/4.1.0/bin64:/opt/hpmpi/bin:/home/qnt/majort/bin/babel/openbabel-2.2.3/bin:/private/chem/bin:/home/qnt/drorimi2/bin:/home/qnt/drorimi2/bin/wham:/home/qnt/drorimi2/bin/perl:.:/home/qnt/drorimi2/anaconda3/bin)  
"

how can this be fixed?  
In general, before I run anything in HADDOCK I do:

"  
cd /home/qnt/drorimi2/software/haddock2.4-2023-01/  
source /home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh  
conda activate /home/qnt/drorimi2/anaconda3/envs/haddock2.4  
./install.csh config.local  
source ./haddock\_configure.csh  
"

but when I added it to the code it did not work

"  
/home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 1: setenv: command not found  
/home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 2: setenv: command not found  
/home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 3: setenv: command not found  
/home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 4: setenv: command not found  
/home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 33: syntax error near unexpected token `"${1}"' /home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh: line 33: ` switch ( “${1}” )’

CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’.  
"

---

<div class="post-metadata">

**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [February 22, 2024, 8:02am UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/4 "2024-02-22T08:02:40Z")

</div>

maybe the issue is that I am not running the sh configuration file?  
when I do that it also doesn’t work. the file looks like  
#!/bin/bash

# 

# HADDOCK configuration file

# 

HADDOCK=“/home/qnt/drorimi2/software/haddock2.4-2023-01”  
HADDOCKTOOLS=“$HADDOCK/tools”  
PYTHONPATH=“${PYTHONPATH}:$HADDOCK”  
alias haddock2.4=“$(which python2.7) $HADDOCK/Haddock/RunHaddock.py”

# 

# Define location of third party software

# 

NACCESS=`which naccess`  
PALES=`which pales`  
PROFIT=`which profit`  
TENSOR2=`which tensor2`

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

is this correct?

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [February 22, 2024, 8:15am UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/5 "2024-02-22T08:15:08Z")

</div>

Define doesn’t work…

---

<div class="post-metadata">

**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [February 22, 2024, 8:42am UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/6 "2024-02-22T08:42:15Z")

</div>

When I run

conda activate haddock2.4  
./install.csh config.local  
source ./haddock\_configure.sh

the error is  
HADDOCK=/home/qnt/drorimi2/software/haddock2.4-2023-01: Command not found.  
HADDOCKTOOLS=/home/qnt/drorimi2/software/haddock2.4-2023-01/tools: Command not found.  
PYTHONPATH=/home/qnt/drorimi2/software/haddock2.4-2023-01:/home/qnt/drorimi2/software/haddock2.4-2023-01:/home/qnt/drorimi2/software/haddock2.4-2023-01: Command not found.  
Illegal variable name.

the haddock\_configure.sh file looks like:  
#!/bin/bash

HADDOCK configuration file  
HADDOCK=“/root/software/haddock2.4-2021-05”  
HADDOCKTOOLS=“$HADDOCK/tools”  
PYTHONPATH=“${PYTHONPATH}:$HADDOCK”  
alias haddock2.4=“$(which python) $HADDOCK/Haddock/RunHaddock.py”  
#alias haddock2.4=“/home/enmr/software/python/bin/python $HADDOCK/Haddock/RunHaddock.py”

Define location of third party software  
NACCESS=which naccess  
PALES=which pales  
PROFIT=which profit  
TENSOR2=which tensor2

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

and config.local  
#!/bin/bash

HADDOCK configuration file  
HADDOCK=“/root/software/haddock2.4-2021-05”  
HADDOCKTOOLS=“$HADDOCK/tools”  
PYTHONPATH=“${PYTHONPATH}:$HADDOCK”  
alias haddock2.4=“$(which python) $HADDOCK/Haddock/RunHaddock.py”  
#alias haddock2.4=“/home/enmr/software/python/bin/python $HADDOCK/Haddock/RunHaddock.py”

Define location of third party software  
NACCESS=which naccess  
PALES=which pales  
PROFIT=which profit  
TENSOR2=which tensor2

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

(priviesly I used ./haddock\_configure.csh and it works, but does not work under the slurm code that looks like this:  
#!/bin/bash

#SBATCH -p prod # Submit to ‘stdmemq’ Partitiion or queue  
#SBATCH -J HADDOCK\_4\_4\_5\_f\_6\_1 # Name the job  
#SBATCH -o MCSA1test-%j.out # Write the standard output to file named ‘jMPItest-\<job\_number\>.out’  
#SBATCH -e MCSA1test-%j.err # Write the standard error to file named ‘jMPItest-\<job\_number\>.err’  
#SBATCH -t 0-10:00:00 # Run for a maximum time of 0 days, 12 hours, 00 mins, 00 secs  
#SBATCH --nodes=1 # Request N nodes  
#SBATCH --ntasks-per-node=18 # Request n cores or task per node  
#SBATCH --mem-per-cpu=1GB # Request 4GB RAM per core

date # prints the date and time

cd /home/qnt/drorimi2/software/haddock2.4-2023-01/  
source /home/qnt/drorimi2/anaconda3/etc/profile.d/conda.csh  
conda activate /home/qnt/drorimi2/anaconda3/envs/haddock2.4  
./install.csh config.local  
source ./haddock\_configure.csh

cd /home/qnt/drorimi2/full\_analize\_40PDB/7pll/HADDOCK/run\_7pll\_4\_4\_5\_flex\_6\_1

#Run full analysis  
haddock2.4 \>&haddock.out

Is this correct? why is the code not working?

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [February 22, 2024, 8:59am UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/7 "2024-02-22T08:59:50Z")

</div>

Are you running under bash or tcsh?  
If the tcsh version work use that one, but then you slurm script must also use tcsh for things to work

I don’t get those errors when trying under bash

You only need to run once the install.csh script.

Try editing your haddock\_configure.sh script and add export commands, e.g.

export HADDOCK=“/root/software/haddock2.4-2021-05”  
export HADDOCKTOOLS=“$HADDOCK/tools”  
export PYTHONPATH=“${PYTHONPATH}:$HADDOCK”  
alias haddock2.4=“$(which python) $HADDOCK/Haddock/RunHaddock.py”Define location of third party software

export PALES=`which pales`  
export PROFIT=`which profit`  
export TENSOR2=`which tensor2`

---

<div class="post-metadata">

**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\
**Post date:** [February 22, 2024, 9:15am UTC](https://ask.bioexcel.eu/t/run-haddock2-4-using-slurm/4855/8 "2024-02-22T09:15:56Z")

</div>

ysing bash  
I changed it to  
#!/bin/bash

# 

# HADDOCK configuration file

# 

export HADDOCK=“/home/qnt/drorimi2/software/haddock2.4-2023-01”  
export HADDOCKTOOLS=“$HADDOCK/tools”  
export PYTHONPATH=“${PYTHONPATH}:$HADDOCK”  
alias haddock2.4=“$(which python2.7) $HADDOCK/Haddock/RunHaddock.py”

# 

# Define location of third party software

# 

#NACCESS=`which naccess`  
#PALES=`which pales`  
#PROFIT=`which profit`  
#TENSOR2=`which tensor2`

export NACCESS=which naccess  
export PALES=which pales  
export PROFIT=which profit  
export TENSOR2=which tensor2

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

and when I run just the file theerror is  
export: Command not found.  
export: Command not found.  
export: Command not found.  
Illegal variable name.