I would like to build a singularity container for an application shipped via AppImage. To do so, I build the following def file:
Bootstrap: docker
From: debian:bullseye-slim
%post
apt-get update -y
apt-get install -y wget unzip fuse libglu1 libglib2.0-dev libharfbuzz-dev libsm6 dbus
cd /opt
wget https://www.ill.eu/fileadmin/user_upload/ILL/3_Users/Instruments/Instruments_list/00_-_DIFFRACTION/D3/Mag2Pol/Mag2Pol_v5.0.2.AppImage
chmod u+x Mag2Pol_v5.0.2.AppImage
%runscript
exec /opt/Mag2Pol_v5.0.2.AppImage
I build the container using singularity build -f test.sif test.def command. The build runs OK but when running the sif file using ./test.sif I get an /.singularity.d/runscript: 3: exec: /opt/Mag2Pol_v5.0.2.AppImage: Permission denied error. Looking inside the container using a singularity shell command shows that the /opt/Mag2Pol_v5.0.2.AppImage executable belongs to root. I guess that it is the source of the problem but I do not know how to solve it. Would you have any idea ?
I am trying to set up PyBOSSA on an AWS EC2 instance running Ubuntu 18.04 LTS. I am following the official instructions and have encountered three errors so far.
sudo apt-get install -y git postgresql postgresql-all postgresql-server-dev-all libpq-dev python-psycopg2 libsasl2-dev libldap2-dev libssl-dev python-virtualenv python-dev build-essential libjpeg-dev libssl-dev libffi-dev dbus libdbus-1-dev libdbus-glib-1-dev libldap2-dev libsasl2-dev python-pip python3-pip redis-server
cd ~
git clone --recursive https://github.com/Scifabric/pybossa
cd pybossa
virtualenv -p python3 env (I'm using Python3 explicitly as my system also has Python 2.7 installed).
source env/bin/activate
pip install -U pip
pip install -r ~/pybossa/requirements.txt
At this point, I start getting error messages... I have copied the stdout and stderr into a file, which I have uploaded here.
I'm not sure if the errors there are what have caused my later errors, but I pushed on through the instructions anyway in hopes it'd work...
cp settings_local.py.tmpl settings_local.py
cp alembic.ini.template alembic.ini
redis-server contrib/sentinel.conf --sentinel
I noted that the Redis server version was 4.0.9 (the instructions say it needs to be v2.6 or greater).
The output from starting the Redis server was as follows:
30284:X 30 Mar 03:09:22.004 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
30284:X 30 Mar 03:09:22.004 # Redis version=4.0.9, bits=64, commit=00000000, modified=0, pid=30284, just started
30284:X 30 Mar 03:09:22.004 # Configuration loaded
...I gather that's ok...
rqscheduler --host 127.0.0.1
This command wasn't installed on my system. I tried to use apt to install it, but there was nothing there. I also tried apt install rq rqscheduler rq-scheduler - nothing found. I then Googled and found the website for rq-scheduler, and found that I could install it by running pip install rq-scheduler
That installed correctly. Nonetheless, running the command rqscheduler --host 127.0.0.1 in the terminal still failed: rqscheduler: command not found.
Knowing that it was a Python package, I wondered if maybe I needed to prepend python3 onto the start of the command: python3 rqscheduler --host 127.0.0.1. Response: python3: can't open file 'rqscheduler': [Errno 2] No such file or directory.
I also tried pip3 install rq-scheduler (which installed fine) and then running the command, but encountered the same error.
I would appreciate knowing how to get that running, but for the purpose of this test, I skipped setting up Regis and the scheduler, and continued with the PyBOSSA instructions:
sudo su postgres
createuser -d -P pybossa
(Password set)
createdb pybossa -O pybossa
exit
python3 cli.py db_create
...and then I got this error:
File "cli.py", line 162
'''SELECT id, created FROM task_run WHERE created LIKE ('\x%')''')
^
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 54-55: truncated \xXX escape
I instead tried python cli.py db_create, just in case it'd work, and got a different error:
python cli.py db_create
ValueError: invalid \x escape
So I'm seeing three separate issues:
Installing the PyBOSSA-required Python packages.
The issue with the rqscheduler command.
The error when starting the PyBOSSA server.
What do these errors mean?
1 ) For the installation, try this:
virtualenv env
source env/bin/activate
sudo apt install python3-pip
pip3 install -r requirements.txt
Which ended with no error.
2) Try :
pip install rq-scheduler==0.9.1
or
pip3 install rq-scheduler==0.9.1
3) The \ char need to be escaped (like \\) in python.
So you may alter the cli.py line 162 (using text editor) from:
'''SELECT id, created FROM task_run WHERE created LIKE ('\x%')''')
To:
'''SELECT id, created FROM task_run WHERE created LIKE ('\\x%')''')
But it will be better to be fixed by dev on github ...
CONCLUSION
According to official documentation,
PYBOSSA for python 3 We’ve finally migrated PYBOSSA to python 3. We’re
not going to merge into master until we test it in production a bit
more, so please, help us by testing it. All you have to do is
basically, check out the python3 branch (migrate-python3) and run it.
Then, any bug, issue you find, you just report it and we will be happy
to help you.
The PYBOSSA python3 version is freshly migrated so finaly is not very stable ... I expect that it will be better to use the PYBOSSA python2.7 branch and follow exactly the documentation.
And according to official github account they try to make money with support (?...)
Get professional support You can hire us to help you with your PYBOSSA
project or server (specially for python 2.7). Go to our website, and
contact us.
The issue has now been fixed for the master branch (https://github.com/Scifabric/pybossa/pull/1986). You can fetch the new code and use it.
I want to build a container from my conda environment following this post. However, I get the following error: '/bin/sh: 1: cannot create ~/.bashrc: Directory nonexistent'. I am using a vagrant VM to build my image and would be grateful for any help.
Editing the .bashrc, aside from failing, will not be helpful as the shell loaded by singularity is explicitly --norc. You want to use the $SINGULARITY_ENVIRONMENT variable in %post to have the values available.
Something along these lines:
%post
# You may need to install some pre-reqs your host system has installed outside of conda, e.g.
# apt update && apt install -y build-essential make zlib
ENV_NAME=$(head -1 environment.yml | cut -d' ' -f2)
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate $ENV_NAME" >> $SINGULARITY_ENVIRONMENT
. /opt/conda/etc/profile.d/conda.sh
conda env create -f environment.yml -p /opt/conda/envs/$ENV_NAME
I listed a few libraries that you probably have installed in your current machine that might not be installed in the slim docker image. You can install them via apt or conda, depending on your preference. If it does happen though, it'll be specific to your environment.yml and host OS, so you'll have to iterate through until the build succeeds.
I'm following the current crystal installation docs, my installation stops at the first moment and give the error:
gpg: connecting dirmngr at '/tmp/apt-key-gpghome.4GKHZljOFL/S.dirmngr' failed: IPC connect call failed
gpg: keyserver receive failed: No dirmngr
I've already installed dirmngr.
First of all, you need to remove crystal.list from sources directory to install from start manually.
sudo rm /etc/apt/sources.list.d/crystal.list
And then:
curl -s "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x09617FD37CC06B54" | sudo apt-key add -
echo "deb https://dist.crystal-lang.org/apt crystal main" > /etc/apt/sources.list.d/crystal.list
sudo apt-get update
sudo apt-get install crystal
I am trying to install Apache HTTP server locally in my box as a regular user (non-root).
I have downloaded Apache 2.4.1 version of Apache HTTP server [http://httpd.apache.org/download.cgi]. However when I am trying to build and install locally in my box I am getting below error:
httpd/httpd-2.4.1 1059> ./configure
checking for chosen layout... Apache
checking for working mkdir -p... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
Configuring Apache Portable Runtime library ...
checking for APR... no
configure: error: APR not found. Please read the documentation.
I am not sure what dependency it is looking for - I mean the download package does not contains it? What I need to do to build / deploy Apache HTTP server?
When it tells you Please read documentation it means that you should go read Apache documentation ( http://httpd.apache.org/docs/2.4/install.html ) which tells you to
download the latest versions of both APR and APR-Util from Apache APR,
unpack them into ./srclib/apr and ./srclib/apr-util (be sure the
domain names do not have version numbers; for example, the APR
distribution must be under ./srclib/apr/)
then do
./configure --with-included-apr
For Ubuntu 11.10 this option seems to be working well:
# APR
wget http://mirrors.axint.net/apache//apr/apr-1.4.6.tar.gz
tar -xvzf apr-1.4.6.tar.gz
cd apr-1.4.6/
./configure
make
make install
cd ..
# APR Utils
wget http://mirrors.axint.net/apache//apr/apr-util-1.4.1.tar.gz
tar -xvzf apr-util-1.4.1.tar.gz
cd apr-util-1.4.1
./configure --with-apr=/usr/local/apr
make
make install
cd ..
# Apache
wget http://apache.petsads.us//httpd/httpd-2.4.1.tar.gz
tar -xvzf httpd-2.4.1.tar.gz
cd httpd-2.4.1
./configure --enable-file-cache --enable-cache --enable-disk-cache --enable-mem-cache --enable-deflate --enable-expires --enable-headers --enable-usertrack --enable-ssl --enable-cgi --enable-vhost-alias --enable-rewrite --enable-so --with-apr=/usr/local/apr/
make
make install
cd ..
You can find more about it below
Source: VaporCreations.com
If you have Debian/Ubuntu you can just:
apt-get install libapr1-dev libaprutil1-dev
Then ./configure
Done
Here are the steps of how I installed apache-httpd on a non-root users:
Download and extract apache-httpd-2.4.2 (but before ./configuring,
making and installing it, follow the steps below:)
Download and extract APR & APR-UTIL into "./srclib/apr" &
"./srclib/apr-util" folders. This requires ./configure
--with-apr=./apache/httpd-2.4.2/srclib/apr (and) --with-included-apr (options).
Download, extract, ./configure (with) --prefix=localURL, make and
make install PCRE into "./pcre" folder. This requires ./configure
--with-pcre=/home/username/apache/pcre (option).
Configure apache-httpd by entring following command (I like to
enable certain options as written in the command below):
./configure --enable-file-cache --enable-cache --enable-disk-cache
--enable-mem-cache --enable-deflate --enable-expires --enable-headers --enable-usertrack --enable-cgi --enable-vhost-alias --enable-rewrite --enable-so --with-apr=/home/username/apache/httpd-2.4.2/srclib/apr --prefix=/home/username/apache/httpd-2.4.2/ --with-included-apr --with-pcre=/home/username/apache/pcre
Note: When configuring apache-httpd, use option "--enable-ssl" ONLY if OpenSSL is installed otherwise DON'T enable it.
Now on the command-line, enter 'make' and 'make install' command.
Open and configure the 'httpd.conf' file e.g.:
"vi /home/eddie_kumar/apache/httpd-2.4.2/conf/httpd.conf"
IMPORTANT: don't forget to change the default port from 80 to something else e.g. 8080, this is especially important for non-root
user. (How to? open httpd.conf -> search "Listen 80" -> change it
to "Listen 8080".
And that's it, now open your browser enter "localhost:8080", it should display "It works!".
If you are using fedora, you can use yum to install APR, APR-Util and PCRE. You'll also need to download apr-devel, apr-util-devel and pcre-devel.
That being said, you can just run the following command on your terminal and no more "configure: error: APR not found.. ..APR-Util and PCRE" errors.
yum -y install arp apr-devel apr-util apr-util-devel pcre pcre-devel
I'm using fedora 17 and planning on using a shell script to setup apache 2.4.3. So yum works pretty slick instead of manually downloading apr, apr-util, and pcre.
1, You need APR (apache portable runtime), which is core component of apache web server
2, If you wnat to do make install, you may need root account
3, Even if not, apache can not start to listen on unprivileged port (lower then 1024) without root account
4, gain root or ask someone with root to install apache from official repo(I don;t know which distro you run) like using yum, apt-get, etc...
Apr or pcre related errors require the source to be downloaded and Apache HTTPD "configure" process needs to be made aware of these source locations on your file system. For instance: if you downloaded the source for APR at ./srclib (relative to apache httpd) then you would use
--with-included-apr
as the configure option.
On the other hand if you want to not build but install APR / APR-UTIL, then you need the following on CentOS / RedHat:
yum install apr-util-devel apr-devel
However it might so happen that the APR version provided by yum does not match what is expected by this version of Apache httpd. In that case you could download APR and APR-UTIL and use the --with-included-apr option.
You could also build PCRE utilizing the same "configure, make, make install" process and then continue where you left off building Apache httpd.
Or you could install pcre:
yum install pcre-devel
If while building PCRE: you see "compile: unrecognized option" then perhaps you would need other dependencies as well: Please see the details at:
http://khanna111.com/wordPressBlog/2012/09/11/94087-2/
It also covers "mod_deflate" and "zlib" as well.
Basic steps
tar -xvf httpd-2.4.1-customized.tar -C ../
#Balancer folder will be created
tar -xvzf openssl-1.0.1.tar.gz -C /balancer/
cd ->/balancer/openssl-1.0.1
./config --prefix=/usr/local/ssl/ shared zlib-dynamic enable-camellia
make depend
make
make install
tar -xvzf pcre-8.30.tar.gz -C ../balancer/
/balancer/pcre-8.30
./configure --prefix=/usr/local/pcre/
make
make install
remove pcre and openssl
Installing and compiling the Apache server on Ubuntu machine
step 1:Install the Java JDK
sudo apt install openjdk-11-jdk
sudo gedit /etc/environment
JAVA_HOME="/usr/lib/jvm/openjdk-11"
source /etc/environment
echo $JAVA_HOME
verify the java version
javac --version
**** install Other required packages:**
sudo apt-get install apache2-dev -y
sudo apt-get install libpcre3 libpcre3-dev
Step 2 :To Install Apache HTTP Server
#1 For ubuntu ,install development tools including the C compiler:
sudo apt-get install build-essential checkinstall
#2 Download and Extract the required files
assuming that all the files have been downloaded into the ~/Downloads directory
Download the Apache HTTP Server httpd-2.4.41.tar.gz from Apache download page (https://httpd.apache.org/download.cgi)
and following required libraries for compiling the apache HTTP server:
apr-1.7.0.tar.gz(http://apr.apache.org/download.cgi)
apr-util-1.6.1.tar.gz(http://apr.apache.org/download.cgi)
pcre2-10.34.tar.gz (ftp://ftp.pcre.org/pub/pcre/) http://pcre.org/
****Read Requirements Section(http://httpd.apache.org/docs/2.4/install.html)***
#3 Extract the tar files
tar -xvf httpd-2.4.41.tar.gz
tar -xvf apr-1.7.0.tar.gz
tar -xvf apr-util-1.6.1.tar.gz
tar -xvf pcre2-10.34.tar.gz
after extraction you should see following list of directories in ~/Downloads
httpd-2.4.41
apr-1.7.0
apr-util-1.6.1
pcre2-10.34
#4 Create a directory for the apache HTTP Server
*make sure to give all rights to this directory so that while compiling files can be read/written
sudo mkdir /home{your username here}/apache
To give all permissions to a apache directory :
sudo chmod -R 777 /home{your username here}/apache
#5 copy the arp and arp-util directory into the ~/Downloads/httpd-2.4.41/srclib/
cd ~/Downloads
mv apr-util-1.6.1 ~/Downloads/httpd-2.4.41/srclib/apr-util
mv apr-1.7.0 ~/Downloads/httpd-2.4.41/srclib/apr
#6 Configure the sources for compilation.
The --prefix option can be used to install the Web server in a location where you can write files.
cd ~/Downloads/httpd-2.4.41/
./configure --prefix=/home/{username here}/apache --with-pcre=~/Downloads/pcre2-10.34
NOTE:
If you have some problems while running above command,you can also try
insallting pcre in /usr/local/pcre, using
./configure --prefix=/usr/local/pcre
make
sudo make install
commands and then by running folllowing commands:
cd ~/Downloads/httpd-2.4.41/
./configure --prefix=/home/{username here}/apache --with-pcre=/usr/local/pcre
make
sudo make install
If you still face some problems ,make sure that ~/apache and its nested directory have read/write permissions. if not run **sudo chmod -R 777 /home{your username here}/apache** command again.
#7 Compile Apache HTTP Server.
cd ~/Downloads/httpd-2.2.25
sudo make
#8 Install Apache HTTP Server.
cd ~/Downloads/httpd-2.2.25
sudo make install
Optional
#9 To Prepare Your Hosts File
sudo gedit /etc/hosts
27.0.0.1 localhost www.example.com
sudo gedit /home/{your username here}/apache/conf/httpd.conf
and copy:
Listen 8000
ServerName www.example.com:8000
#10 Test the installation to ensure Apache HTTP Server is working.
/home/{your username here}//apache/bin/apachectl -k start