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DMR Identification Tool
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Segmentation fault of HOME #13

Closed Linhua-Sun closed 6 years ago

Linhua-Sun commented 6 years ago

Hi: I follow the instructions to install HOME software. But IT will give me segmentation fault (core dumped) error (when using HOME-pairwise or HOME-timeseries). And nothing else.

Akanksha2511 commented 6 years ago

Hi, Are you using virtual env to install it ?. Can you please check if, after installation, you get the help message when you type HOME-pairwise or HOME-timeseries.

Linhua-Sun commented 6 years ago

Thank you very much! I didn't use virtual env to install HOME. Since I also use python 2.7. Is it necessary to use virtual env to install? Why? I will try 'virtual env' again. And I didn't get the help messages after the type of HOME-pairwise or HOME-timeseries.

Linhua-Sun commented 6 years ago

Sorry, after I retry to install HOME follow the instructions (use the virtual env to install ) completely. It gives me another error. As following:

Traceback (most recent call last):
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
    __import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1518, in run_script
    .format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/HOME-pairwise' not found in metadata at '/data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/HOME.egg-info'

Thank you very much!

Akanksha2511 commented 6 years ago

Hi, seems like the package is not installed successfully. Did you get any error message after running python setup.py install ?. Also please make sure you cd in the HOME directory before starting the run.

Linhua-Sun commented 6 years ago

Hi, you can see it seems that the installation is successful. I didn't see any error messages duing installation. And sure, I cd into the HOME dir.

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to HOME.egg-info/requires.txt
writing HOME.egg-info/PKG-INFO
writing top-level names to HOME.egg-info/top_level.txt
writing dependency_links to HOME.egg-info/dependency_links.txt
reading manifest file 'HOME.egg-info/SOURCES.txt'
writing manifest file 'HOME.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/__init__.py -> build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/HOME_functions.py -> build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/HOME_timeseries_functions.py -> build/bdist.linux-x86_64/egg/HOME
byte-compiling build/bdist.linux-x86_64/egg/HOME/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/HOME/HOME_functions.py to HOME_functions.pyc
byte-compiling build/bdist.linux-x86_64/egg/HOME/HOME_timeseries_functions.py to HOME_timeseries_functions.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/HOME-timeseries -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/HOME-pairwise -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/HOME-timeseries to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/HOME-pairwise to 775
copying HOME.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/HOME-0.4-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing HOME-0.4-py2.7.egg
Removing /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg
Copying HOME-0.4-py2.7.egg to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
HOME 0.4 is already the active version in easy-install.pth
Installing HOME-pairwise script to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin
Installing HOME-timeseries script to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin

Installed /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg
Processing dependencies for HOME==0.4
Searching for statsmodels==0.6.1
Best match: statsmodels 0.6.1
Adding statsmodels 0.6.1 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for scikit-learn==0.16.1
Best match: scikit-learn 0.16.1
Adding scikit-learn 0.16.1 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for scipy==0.16.0
Best match: scipy 0.16.0
Adding scipy 0.16.0 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for pandas==0.17.1
Best match: pandas 0.17.1
Adding pandas 0.17.1 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for numpy==1.13.3
Best match: numpy 1.13.3
Adding numpy 1.13.3 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for python-dateutil==2.6.1
Best match: python-dateutil 2.6.1
Adding python-dateutil 2.6.1 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for pytz==2017.3
Best match: pytz 2017.3
Adding pytz 2017.3 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for six==1.11.0
Best match: six 1.11.0
Adding six 1.11.0 to easy-install.pth file

Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Finished processing dependencies for HOME==0.4
Akanksha2511 commented 6 years ago

Hi, the installation looks fine. Can you please check if your virtual environment (hh) bin contains HOME-pairwise and HOME-timeseries binaries, something like below: bin

Linhua-Sun commented 6 years ago

Yes, you can see it is there: 

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$pwd
/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$l
total 68K
-rwxrwxr-x 1 linhua linhua 9.9K Dec 13 17:22 python
lrwxrwxrwx 1 linhua linhua    6 Dec 13 17:22 python2.7 -> python
lrwxrwxrwx 1 linhua linhua    6 Dec 13 17:22 python2 -> python
-rwxrwxr-x 1 linhua linhua  269 Dec 13 17:22 easy_install-2.7
-rwxrwxr-x 1 linhua linhua  269 Dec 13 17:22 easy_install
-rwxrwxr-x 1 linhua linhua  241 Dec 13 17:22 pip2.7
-rwxrwxr-x 1 linhua linhua  241 Dec 13 17:22 pip2
-rwxrwxr-x 1 linhua linhua  241 Dec 13 17:22 pip
-rwxrwxr-x 1 linhua linhua  248 Dec 13 17:22 wheel
-rw-rw-r-- 1 linhua linhua 1.2K Dec 13 17:22 activate_this.py
-rw-rw-r-- 1 linhua linhua 2.2K Dec 13 17:22 activate.fish
-rw-rw-r-- 1 linhua linhua 1.1K Dec 13 17:22 activate.csh
-rw-rw-r-- 1 linhua linhua 2.1K Dec 13 17:22 activate
-rwxrwxr-x 1 linhua linhua 2.4K Dec 13 17:22 python-config
-rwxrwxr-x 1 linhua linhua  793 Dec 13 17:27 f2py
-rwxrwxr-x 1 linhua linhua  201 Dec 13 20:07 HOME-pairwise
-rwxrwxr-x 1 linhua linhua  205 Dec 13 20:07 HOME-timeseries
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$
Akanksha2511 commented 6 years ago

Can you please send me what you get by following commands : (hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ ls

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ HOME-pairwise

Linhua-Sun commented 6 years ago

Thank you so much:

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$cd /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ls
HOME  HOME.egg-info  README.md  build  dist  environment.yml  requirements.txt  saved_model  scripts  setup.py  testcase  training_data
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$HOME-pairwise
Traceback (most recent call last):
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
    __import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1518, in run_script
    .format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/HOME-pairwise' not found in metadata at '/data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/HOME.egg-info'
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$
Akanksha2511 commented 6 years ago

The issue is it's not able to find HOME-pairwise in scripts. Can you please do the following to check if the binaries are present in script: (hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ cd ./scripts/ and then ls

Also, please just try deactivating and reactivatiing your virtual env.

Linhua-Sun commented 6 years ago

You can see there are those binaries files.

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/scripts]$l
total 56K
-rwxrwxrwx 1 linhua linhua 1.3K Dec 13 17:24 HOME_R_time.R
-rwxrwxrwx 1 linhua linhua 1.4K Dec 13 17:24 HOME_R.R
-rwxrwxrwx 1 linhua linhua  23K Dec 13 17:24 HOME-timeseries
-rwxrwxrwx 1 linhua linhua  22K Dec 13 17:24 HOME-pairwise

And I exit the shell and login in again, then reactivate my virtual env. But it still not works. And new errors generated after I chmod 777 the HOME-pairwise and other files. I see that they don't have run permission.

Traceback (most recent call last):
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
    __import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1534, in run_script
    exec(script_code, namespace, namespace)
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg/EGG-INFO/scripts/HOME-pairwise", line 18, in <module>

  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/__init__.py", line 48, in <module>
    from pandas.io.api import *
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/io/api.py", line 15, in <module>
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/io/packers.py", line 63, in <module>
    from pandas.msgpack import Unpacker as _Unpacker, Packer as _Packer, ExtType
  File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/msgpack/__init__.py", line 21, in <module>
    from pandas.msgpack._packer import Packer
ImportError: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /home/linhua/.linuxbrew/lib/libstdc++.so.6)

Thank you very much!

Akanksha2511 commented 6 years ago

I guess you have installed HOME inside your virtual environment and that's why you are getting permission issue. Can you please make sure HOME directory is installed "outside" the virtual env as below. file_structure HOME_env is the virtual env name. In your case it will be hh.

Linhua-Sun commented 6 years ago

Wow, it seems to be the key point. I will have a try immediately.

Linhua-Sun commented 6 years ago

Sorry for the wrong reply. I am sure that HOME directory is installed "outside" the virtual env. You can see following:

(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY]$l
total 8.0K
drwxrwxr-x  5 linhua linhua 4.0K Dec 13 17:22 hh
drwxrwxr-x 11 linhua linhua 4.0K Dec 13 17:27 HOME
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY]$l *
hh:
total 16K
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:22 include
drwxrwxr-x 3 linhua linhua 4.0K Dec 13 17:22 lib
-rw-rw-r-- 1 linhua linhua   60 Dec 13 17:22 pip-selfcheck.json
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 20:07 bin

HOME:
total 60K
-rw-rw-r-- 1 linhua linhua   74 Dec 13 17:24 requirements.txt
-rw-rw-r-- 1 linhua linhua  146 Dec 13 17:24 environment.yml
-rw-rw-r-- 1 linhua linhua  13K Dec 13 17:24 README.md
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 HOME
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 saved_model
-rw-rw-r-- 1 linhua linhua  511 Dec 13 17:24 setup.py
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 scripts
drwxrwxr-x 4 linhua linhua 4.0K Dec 13 17:24 testcase
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 training_data
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:27 HOME.egg-info
drwxrwxr-x 5 linhua linhua 4.0K Dec 13 17:27 build
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:27 dist
Akanksha2511 commented 6 years ago

Hi, your virtual environment doesn't seem to have local and share directory as in the example I sent earlier. Also, it has an extra include directory. Can you please make sure you follow the steps for setting up the virtual environment correctly. Thanks