BASH: parallel run

I have a bash script that takes as input three arrays with equal length: METHODS, INFILES and OUTFILES.

This script will let METHODS[i] solves problem INFILES[i] and saves the result to OUTFILES[i], for all indices i (0 <= i <= length-1).

Each element in METHODSis a string of the form:

$HOME/program/solver -a <method>

where solver is a program that can be called as follows:

$HOME/program/solver -a <method> -m <input file> -o <output file> --timeout <timeout in seconds>

The script solves all the problems in parallel and set the runtime limit for each instance to 1 hour (some methods can solve some problems very quickly though), as follows:

#!/bin/bash
source METHODS
source INFILES
source OUTFILES

start=`date +%s`

## Solve in PARALLEL
for index in ${!OUTFILES[*]}; do 
    (alg=${METHODS[$index]}
    infile=${INFILES[$index]}
    outfile=${OUTFILES[$index]}

    ${!alg}  -m $infile -o $outfile --timeout 3600) &
done
wait


end=`date +%s`

runtime=$((end-start))
echo "Total runtime = $runtime (s)"
echo "Total number of processes = ${#OUTFILES[@]}"

In the above I have length = 619. I submitted this bash to a cluster with 70 available processors, which should take at maximum 9 hours to finish all the tasks. This is not the case in reality, however. When using the top command to investigate, I found that only two or three processes are running (state = R) while all the others are sleeping (state = D).

What am I doing wrong please?

Furthermore, I have learnt that GNU parallel would be much better for running parallel jobs. How can I use it for the above task?

Thank you very much for your help!

Update: My first try with GNU parallel:

The idea is to write all the commands to a file and then use GNU parallel to execute them:

#!/bin/bash
source METHODS
source INFILES
source OUTFILES

start=`date +%s`    

## Write to file
firstline=true
for index in ${!OUTFILES[*]}; do 
    (alg=${METHODS[$index]}
    infile=${INFILES[$index]}
    outfile=${OUTFILES[$index]}
    if [ "$firstline" = true ] ; then
        echo "${!alg}  -m $infile -o $outfile --timeout 3600" > commands.txt
        firstline=false
    else
        echo "${!alg}  -m $infile -o $outfile --timeout 3600" >> commands.txt
    fi
done

## Solve in PARALLEL
time parallel :::: commands.txt

end=`date +%s`

runtime=$((end-start))
echo "Total runtime = $runtime (s)"
echo "Total number of processes = ${#OUTFILES[@]}"

What do you think?

Update 2: I'm using GNU parallel and having the same problem. Here's the output of top:

top - 02:05:25 up 178 days,  8:16,  2 users,  load average: 62.59, 59.90, 53.29
Tasks: 596 total,   7 running, 589 sleeping,   0 stopped,   0 zombie
Cpu(s): 12.9%us,  0.9%sy,  0.0%ni, 63.3%id, 22.9%wa,  0.0%hi,  0.1%si,  0.0%st
Mem:  264139632k total, 260564864k used,  3574768k free,     4564k buffers
Swap: 268420092k total, 80593460k used, 187826632k free,    53392k cached

  PID USER     PR  NI  VIRT  RES  SHR S %CPU %MEM   TIME+   COMMAND
28542 khue     20   0 7012m 5.6g 1816 R  100  2.2  12:50.22 opengm_min_sum
28553 khue     20   0 11.6g  11g 1668 R  100  4.4  17:37.37 opengm_min_sum
28544 khue     20   0 13.6g 8.6g 2004 R  100  3.4  12:41.67 opengm_min_sum
28549 khue     20   0 13.6g 8.7g 2000 R  100  3.5   2:54.36 opengm_min_sum
28551 khue     20   0 11.6g  11g 1668 R  100  4.4  19:48.36 opengm_min_sum
28528 khue     20   0 6934m 4.9g 1732 R   29  1.9   1:01.13 opengm_min_sum
28563 khue     20   0 7722m 6.7g 1680 D    2  2.7   0:56.74 opengm_min_sum
28566 khue     20   0 8764m 7.9g 1680 D    2  3.1   1:00.13 opengm_min_sum
28530 khue     20   0 5686m 4.8g 1732 D    1  1.9   0:56.23 opengm_min_sum
28534 khue     20   0 5776m 4.6g 1744 D    1  1.8   0:53.46 opengm_min_sum
28539 khue     20   0 6742m 5.0g 1732 D    1  2.0   0:58.95 opengm_min_sum
28548 khue     20   0 5776m 4.7g 1744 D    1  1.9   0:55.67 opengm_min_sum
28559 khue     20   0 8258m 7.1g 1680 D    1  2.8   0:57.90 opengm_min_sum
28564 khue     20   0 10.6g  10g 1680 D    1  4.0   1:08.75 opengm_min_sum
28529 khue     20   0 5686m 4.4g 1732 D    1  1.7   1:05.55 opengm_min_sum
28531 khue     20   0 4338m 3.6g 1724 D    1  1.4   0:57.72 opengm_min_sum
28533 khue     20   0 6064m 5.2g 1744 D    1  2.1   1:05.19 opengm_min_sum

(opengm_min_sum is the solver above)

I guess that some processes consume so much resource that the others do not have anything left and enter the D state?