Bash script not installing python packages properly

Question

I've been following this tutorial to install openacc locally on my jetson tk1 and I'm finding the install script to be incorrect. I didn't see any errors when I compiled the openacc library, however when I attempt to compile I get an error that says

ubuntu@tegra-ubuntu:~/apps/acc/accull/yacf/examples/acc$ accull -v -o gpu.x  acc_test.c 
 **************************************** 
                 _    _ _      _          
                | |  | | |    | |         
   __ _  ___ ___| |  | | |    | |         
  / _` |/ __/ __| |  | | |    | |         
 | (_| | (_| (__| |__| | |____| |____     
  \__,_|\___\___|\____/|______|______|    
 **************************************** 
 Release 0.4alpha 

* Verbose output
* Output executable name gpu.x
* Processing acc_test.c to ./accull_k3Ty8/acc_test.c
* Building acc_test.c
* Running StS translation 
Traceback (most recent call last):
  File "/home/ubuntu/apps/acc/accull/yacf//bin/c2frangollo.py", line 64, in <module>
    from Backends.Frangollo.Mutators.Common import FrangolloMutatorError
  File "/home/ubuntu/apps/acc/accull/yacf/Backends/Frangollo/Mutators/Common.py", line 33, in <module>
    from Backends.C99.Visitors.LlcFilters import AccScopeReverse, AccScopeFilter
  File "/home/ubuntu/apps/acc/accull/yacf/Backends/C99/Visitors/LlcFilters.py", line 40, in <module>
    from Tools.Tree import NodeNotFound
  File "/home/ubuntu/apps/acc/accull/yacf/Tools/Tree.py", line 34, in <module>
    c_ast = getCurrentLanguageAst()
  File "/home/ubuntu/apps/acc/accull/yacf/Frontend/Shortcuts.py", line 40, in getCurrentLanguageAst
    myclass = __import__(config.FRONTEND_MODULE + '.' + str(name) + "." + str(name).lower() + '_ast', globals(), locals(), [str(name),])
  File "/home/ubuntu/apps/acc/accull/yacf/Frontend/C99/__init__.py", line 16, in <module>
    from .c99_parser import C99Parser
  File "/home/ubuntu/apps/acc/accull/yacf/Frontend/C99/c99_parser.py", line 15, in <module>
    import ply.yacc
ImportError: No module named ply.yacc
! Compilation of acc_test.c FAILED (no Project directory build )
/usr/local/cuda/bin/nvcc -Xcompiler -fopenmp -lrt -lcuda -lOpenCL -lrt -lcuda -arch=sm_20 *.o /home/ubuntu/apps/acc/accull/frangollo/src/libfrangollo.a -o gpu.x
nvlink fatal   : Could not open input file '*.o'
* Finished

http://scelementary.com/2015/04/30/openacc-on-jetson-tk1.html

#!/bin/bash

ACCULLROOT=/home/ubuntu/apps/acc

mkdir -p $ACCULLROOT/source
cd $ACCULLROOT/source

wget https://www.python.org/ftp/python/2.7.9/Python-2.7.9.tar.xz
wget https://pypi.python.org/packages/source/S/Sphinx/Sphinx-1.3.1.tar.gz
wget http://lxml.de/files/lxml-3.4.2.tgz
wget http://www.dabeaz.com/ply/ply-3.4.tar.gz
wget https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz

tar xvf Python-2.7.9.tar.xz
cd Python-2.7.9/
./configure --prefix=$ACCULLROOT
make -j2 
make install

list=(Sphinx-1.3.1.tar.gz lxml-3.4.2.tgz ply-3.4.tar.gz Mako-1.0.1.tar.gz)
for file in $list
do
  if [ "$file" == "*.tgz" ] 
    name=$(basename $file .tgz)
  then
    name=$(basename $file .tar.gz)
  fi

  tar zxvf $file
  cd $basename
  $ACCULLROOT/bin/python setup.py build
  $ACCULLROOT/bin/python setup.py install
  cd ..

done

You might have to run the script as root/sudo. You could also try to install `ply` manually. `pip install ply` — Håken Lid, Jan 30 '16 at 18:16

Rany Albeg Wein · Accepted Answer · 2016-01-31T04:38:41.687

There are several problems:

You initialize an array called list but you attempt to iterate over its elements like this for file in $list which will only iterate over the first element, since $list is like ${list[0]}. Use for file in "${list[@]}" to iterate over the complete array.
Don't forget to double-quote your expansions to prevent Globbing and WordSplitting. For example name=$(basename $file .tar.gz) or tar zxvf $file will yield unwanted results in case the the value of the variable file contains white-spaces and is left without double-quotes ( i.e. $file instead of the correct form: "$file" )
I guess that you mistakenly used cd $basename instead of cd "$name" - or something else, if it doesnt make sense. Anyhow the variable name appears to be unused.
This line [ "$file" == "*.tgz" ] is probably wrong. It seems that the writer is attempting to match "$file" against a glob pattern. Well, in order to do that, two things must change: 1. Use [[ instead of [, since the command [ simply does not support glob matching. 2. The double-quotes around *.tgz should be removed - otherwise, "$file" will be matched against a literal *.tgz. So to summarize 1 and 2, the script should use [[ $file = *.tgz ]] instead of [ "$file" == "*.tgz" ]. I encourage you to read further about TestsAndConditionals and to see this great FAQ, which is a part of this Bash Guide - probably one of the best ( if not the only ) source to learn Bash from.
The script does not check whether cd exited successfully, and simply continues on. It can give unwanted results. cd || exit is prefered, but modify it to be descriptive to the user.
Regarding the variable ACCULLROOT : By convention, environment variables (PATH, EDITOR, SHELL, ...) and internal shell variables (BASH_VERSION, RANDOM, ...) are fully capitalized. All other variable names should be lowercase. Since variable names are case-sensitive, this convention avoids accidentally overriding environmental and internal variables.

I didn't see this before and I've seen found an alternative to openacc but thank you for this detailed reply! — Zypps987, Oct 22 '16 at 06:27

Bash script not installing python packages properly

1 Answers1