sfennell2
commented
2 years ago @ddj116 I followed your steps exactly and I am not getting an invalid read. Can I please see the output of your ./configure step?
Open ddj116 opened 2 years ago
sfennell2
commented
2 years ago @ddj116 I followed your steps exactly and I am not getting an invalid read. Can I please see the output of your ./configure step?
ddj116
commented
2 years ago Sure, here's the output of ./configure:
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... -std=gnu11
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -E
checking for X... libraries , headers
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for X11/Intrinsic.h... yes
checking for trick_source/data_products/fermi-ware... no
checking for main in -lxml2... yes
checking for libxml/tree.h... yes
checking for gawk... gawk
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) -std=gnu11
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for g++ option to enable C++11 features... (cached) none needed
checking gcc version... 4.8.5
checking gcc version >= 4.8... yes
which: invalid option -- 's'
which: invalid option -- 't'
which: invalid option -- 'd'
which: invalid option -- '='
which: invalid option -- 'g'
which: invalid option -- 'n'
which: invalid option -- 'u'
which: invalid option -- '1'
which: invalid option -- '1'
checking for tee... /usr/bin/tee
checking for ld... /usr/bin/ld
checking for flex... flex
checking for lex output file root... lex.yy
checking for lex library... none needed
checking for library containing yywrap... no
checking whether yytext is a pointer... yes
checking for bison... /usr/bin/bison
checking for curl... /usr/bin/curl
checking for perl... /usr/bin/perl
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for perl version... 5.16.3
checking for zip... /usr/bin/zip
checking for python3... /local/<user>/trick_issue_XYZ/.venv/bin/python3
checking for python3.6-config... /usr/bin/python3.6-config
checking for gnuplot... /usr/bin/gnuplot
checking for swig... /usr/bin/swig
checking SWIG version... 2.0.10
checking for SWIG library... /usr/share/swig/2.0.10
checking for gawk... (cached) gawk
checking for javac... javac
checking javac version >= 1.8... yes
checking for mvn... /usr/bin/mvn
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for egrep... /usr/bin/grep -E
checking whether /usr/bin/gcc is Clang... no
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for perl module Text::Balanced... ok
checking for perl module Digest::MD5... ok
checking for llvm-config... /bin/llvm-config
checking for /usr/include/clang/Basic/LLVM.h... yes
checking for /usr/lib64/llvm/libLLVMSupport.a... yes
checking for clang... /usr/bin/clang
checking for /usr/lib64/llvm/libclangFrontend.a... yes
checking clang version >= 3.4.2... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... yes
checking for udunits2.h... no
checking for udunits2/udunits2.h... yes
checking for main in -ludunits2... yes
checking for hdf5.h... yes
checking for main in -lhdf5... yes
checking for gsl/gsl_rng.h... yes
checking for main in -lgsl... yes
checking for gtest/gtest.h... yes
checking for civetweb.h... no
configure: creating ./config.status
config.status: creating share/trick/makefiles/config_user.mk
configure script successfully completedAnd here's how the virtual environment manages the python3 version:
(.venv) user@user: /local/user/trick_issue_XYZ > ll .venv/bin/
total 32
-rw-r--r-- 1 user user 2215 Jul 22 13:01 activate
-rw-r--r-- 1 user user 1271 Jul 22 13:01 activate.csh
-rw-r--r-- 1 user user 2435 Jul 22 13:01 activate.fish
-rwxr-xr-x 1 user user 267 Jul 22 13:01 easy_install
-rwxr-xr-x 1 user user 267 Jul 22 13:01 easy_install-3.6
-rwxr-xr-x 1 user user 239 Jul 22 13:01 pip
-rwxr-xr-x 1 user user 239 Jul 22 13:01 pip3
-rwxr-xr-x 1 user user 239 Jul 22 13:01 pip3.6
lrwxrwxrwx 1 user user 7 Jul 22 13:01 python -> python3
lrwxrwxrwx 1 user user 16 Jul 22 13:01 python3 -> /usr/bin/python3
(.venv) user@user: /local/user/trick_issue_XYZ > which python
/local/user/trick_issue_XYZ/.venv/bin/python
(.venv) user@user: /local/user/trick_issue_XYZ > python --version
Python 3.6.8I've got some more information since y'all are having trouble reproducing this. In the Trick lab the machine cordonbleu is CentOS 7.9, closely resembling the platform in which I see these errors in the FSL. I was unable to produce the error on that machine, which was surprising. Comparing the output of trick's ./configure I noticed the only real difference being SWIG versions:
In FSL, the system swig is 2.0.10 which configure picks up by default. Unfortunately, even when switching swig over to 3.0.12 (/software/x86_64/swig/3.0.12/bin/) I'm still getting 121 Invalid read errors similar to those shown above. The following script can be run in the FSL to reproduce this issue:
#!/bin/bash
mkdir trick_issue_1312/ && cd trick_issue_1312 # Create a workspace
python3 -m venv .venv && source .venv/bin/activate # Create python3 venv
git clone https://github.com/nasa/trick.git # Get trick
cd trick && git checkout 19.4.0 # Checkout to latest
./configure --with-swig=/software/x86_64/swig/3.0.12/bin/ && make >& trick_build.txt # Build trick
cd trick_sims/Ball/SIM_ball_L1 && ../../../bin/trick-CP # Build sim
valgrind ./S_main_Linux*.exe RUN_test/input.py >& valgrind_out.txt
spfennell
The errors
Error signature looks like this, about 126 instances with
SIM_ball_L1:How to replicate
This little script will replicate the issue. I ran this on FSL (CentOS 7.9) with
gcc4.8.5 but have also observed it withgcc8.3.0 in my Gateway simulation andgcc4.8.5 in my Ramtares simulation.This appears to be related to use of
python3-- withpython2I don't see any of these errors in my Ramtares project.FYI @spfennell @jmpenn @jdeans289 -- If you have trouble replicating or other questions please let me know.