problems with init_vars

[Bea9619]

Hi everyone,
I previously asked for this problem in the issues section. Now I post it here. Following @shen4brains advice, I bound the Freesurfer local directory to the container and the relative problem is now solved. However, now running init_vars, another issue came out with the singularity run command

init_vars: line 126: source: activate: file not found

The command looks for SOFTDIR directory, which at line 68 is defined as:
export SOFTDIR=/opt/tvb-pipeline #TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)

At line 34 FSL is defined as:
export FSLDIR=/opt/fsl #TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)

However, no problems arise from FSL, since it seems that the path to opt directory is the default option for singularity (as for SOFTDIR).
How should we proceed?
Thanks

Beatrice

[justinliuyuwang]

Hi Beatrice!

Can I ask what container you are using and may I see 1) the contents of your init_var file and 2) the command you use to launch the container?

Thank you!
Justin

[Bea9619]

Hi Justin!
Sorry for the delay in my reply.
We are using the tvb-ukbb_latest.sif container
We run the following command:
singularity run -B /home -B /usr/local /home/psicobiologia/ANALISI/prova/container_tvb/tvb-ukbb_latest.sif sogg_1 /home/psicobiologia/ANALISI/prova/container_tvb/tvb-ukbb
We add -B /usr/local in order to make it possible to bound our local Freesurfer installation folder (as we pointed to in init_vars).
Our init_vars file looks like

# UKBB ROOT DIR LOCATION
export BBDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd ..; pwd )"

#SETUP FSL  
export FSLDIR=/opt/fsl                                       			#TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)
. $FSLDIR/etc/fslconf/fsl.sh
export FSLCONFDIR="${FSLDIR}/config"
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLGECUDAQ=cuda.q                                                        #TO BE MODIFIED BY USER

#TODO implement this in the files
export QUEUE_STANDARD="all.q"                                                   #TO BE MODIFIED BY USER
export QUEUE_MORE_MEM="bigmem_16.q"                                             #TO BE MODIFIED BY USER
export QUEUE_MAX_MEM="bigmem_64.q"                                              #TO BE MODIFIED BY USER

# option 1: true; use full-GPU probtrackx call. default.
# option 2: gpu_batch; split GPU probtrackx into 10 smaller batches.
#           for low-memory systems.
# option 3: false: use CPU probtrackx split into 10 smaller batches.
#           use for systems without CUDA GPU
export PROBTRACKX_GPU="true"

export REPARCELLATE="false" #TO BE MODIFIED BY USER

#SETUP AFNI
#export AFNIDIR=/opt/afni                                                        #TO BE MODIFIED BY USER
#export AFNIDIR="/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/gcc9/afni/20.3.05"

#SETUP FREESURFER 
export FREESURFER_HOME="/usr/local/freesurfer"                                      #TO BE MODIFIED BY USER

# if usin on Compute Canada, load module first
#source $EBROOTFREESURFER/FreeSurferEnv.sh
source $FREESURFER_HOME/SetUpFreeSurfer.sh  > /dev/null

#SETUP ANTS
export ANTSPATH="/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/gcc9/ants/2.3.5/bin"

export SOFTDIR=/opt/tvb-pipeline						#TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)


# SET UP MATLAB
export MCROOT="/opt/mcr"							#TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)
export MCRV="v93"

#Move $FSLDIR/bin before $FREESURFER_HOME in the path
FSLDIRseddable=`echo $FSLDIR | sed 's|/|\\\/|g'`
PATH=`echo $PATH | sed "s|$FSLDIR/bin||g"`
export PATH="$FSLDIR/bin:$PATH"

#SETUP EXTERNAL LIBRARIES
export R_LIBS="/usr/lib/R/library"						#TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)	
export R_DIR="/usr/lib/R"							#TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)


#SET LOCALE FOR FLOATING POINT FORMATTING
export LC_ALL=C

#ENV VARIABLES FOR BIOBANK
export BB_BIN_DIR="$BBDIR/tvb-ukbb"
export FSLGPUDIR="$BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx"
export MNI="$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz"
export MNI_mask="$FSLDIR/data/standard/MNI152_T1_1mm_brain_mask.nii.gz"
export MNI_brain="$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz"
export MNI_dir="$FSLDIR/data/standard"
export templ="$BB_BIN_DIR/templates"
export PYTHONPATH="$SOFTDIR/software/env/bin/python"

export FSL_FIXDIR="$BB_BIN_DIR/bb_functional_pipeline/bb_fix_dir"
export PARC_IMG="$templ/parcellations/TVB_SchaeferTian/TVB_SchaeferTian_420.nii.gz"                      #TO BE MODIFIED BY USER
export PARC_LUT="$templ/parcellations/TVB_SchaeferTian/TVB_SchaeferTian_420_LUT.tsv"                     #TO BE MODIFIED BY USER
export PARC_NAME="TVBSchaeferTian420"				#TO BE MODIFIED BY USER
export SUSCEPT_ROIS="$templ/parcellations/TVB_SchaeferTian/SusceptibilityROIs_SchaeferTian_420.nii.gz"                     		#TO BE MODIFIED BY USER
# export numROI="436"                                                              #TO BE MODIFIED BY USER
export TRAINING_FILE="ADNI3_Training.RData"                                            #TO BE MODIFIED BY USER
export SynB0="y"                                            #TO BE MODIFIED BY USER
export PE_direction="0 -1 0"                                            #TO BE MODIFIED BY USER
export topupValue="0.1"					#TO BE MODIFIED BY USER - leave empty "" for no value
export topupValue_default="0.1"					#TO BE MODIFIED BY USER - leave empty "" for no value
export EPIfactor="50"					#TO BE MODIFIED BY USER

# set to 1 for single shell diffusion data and 2 for multi-shell
export DIFF_SHELL_TYPE="1"

#INCLUDE 3 MAIN BIOBANK DIRECTORIES IN PATH
export PATH="$BB_BIN_DIR/bb_pipeline_tools/:$BB_BIN_DIR/bb_general_tools/:$PATH"


#SET PATH FOR MCR
export LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$MCROOT/$MCRV/runtime/glnxa64:$MCROOT/$MCRV/bin/glnxa64:$MCROOT/$MCRV/sys/os/glnxa64:$MCROOT/$MCRV/sys/opengl/lib/glnxa64:$LD_LIBRARY_PATH"

export MATLAB_COMPILER_RUNTIME="$MCROOT/$MCRV"

export XAPPLRESDIR="$MCROOT/$MCRV/X11/app-defaults"

# source activate $SOFTDIR/software/env
source activate $SOFTDIR/software/env

The error is
/home/psicobiologia/ANALISI/prova/container_tvb/tvb-ukbb/init_vars: line 126: source: activate: file not found

As you can see line 126 call SOFTDIR directory, that in init_vars is defined as
export SOFTDIR=/opt/tvb-pipeline #TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY)

How can we proceed?
Many thanks

Beatrice

[justinliuyuwang]

Hi Beatrice! Sorry for the wait on the reply.

If you run apptainer shell tvb-ukbb_latest.sif you should be in the container. Once you've done that, does the following run without error?

export SOFTDIR="/opt/tvb-pipeline"
source activate $SOFTDIR/software/env

Also, while you're in the container, does /opt/tvb-pipeline/software/env exist or does ls /opt/tvb-pipeline/software/env result in No such file or directory or some other error?