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 have hosted one docker with PHP in a shared server of our office environments. Previously it was working fine without any issue. All the users were able to access the site via port forwarding to 8080. Here is my docker file details -
# Choose Repo from Docker Hub
FROM centos:latest
# Provide details of maintainer
MAINTAINER ritu
#Install necessary software
RUN yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
RUN yum -y install http://rpms.remirepo.net/enterprise/remi-release-7.rpm
RUN yum -y install yum-utils
RUN yum-config-manager --enable remi-php56
RUN yum -y install php php-mcrypt php-cli php-gd php-curl php-mysql php-ldap php-zip php-fileinfo php-devel php-pear make gcc systemtap-sdt-devel httpd unzip postfix
RUN export PHP_DTRACE=yes
RUN curl -sS https://getcomposer.org/installer | php
RUN mv -f composer.phar /usr/local/bin/composer
RUN chmod +x /usr/local/bin/composer
RUN composer require phpmailer/phpmailer
COPY phpinfo.php /var/www/html/
COPY php.ini /var/www/
COPY httpd.conf /var/www/
RUN cp -f /var/www/httpd.conf /etc/httpd/conf/
COPY *.rpm /var/www/
#Install & Configure OCI for PHP
COPY oci8-2.0.12.tgz /
RUN tar -xvf oci8-2.0.12.tgz
RUN yum -y localinstall /var/www/*.rpm --nogpgcheck
COPY client.sh /etc/profile.d/
RUN chmod +x /etc/profile.d/client.sh
RUN cp -f /var/www/php.ini /etc/
COPY php_oci8_int.h oci8-2.0.12/
COPY Log_Check.zip /
RUN unzip Log_Check.zip
RUN cp -a -R /Log_Check/* /var/www/html/
WORKDIR /oci8-2.0.12
RUN phpize
RUN ./configure --with-oci8=/usr/lib/oracle/12.2/client64
RUN cp -f /usr/include/oracle/12.2/client64/*.h /oci8-2.0.12/include/
RUN make
RUN make install
RUN ls /var/www/html/
RUN rm -rf /var/run/apache2/apache2.pid
#Expose necessary ports
EXPOSE 80
EXPOSE 1521
EXPOSE 25
#Provide Entrypoint
CMD ["-D", "FOREGROUND"]
ENTRYPOINT ["/usr/sbin/httpd"]
Suddenly one of my friend added another docker with same port 8080 in the same server. After that my docker got stopped. with below error -
AH00558: httpd: Could not reliably determine the server's fully qualified domain name, using 172.18.0.3. Set the 'ServerName' directive globally to suppress this message
httpd (pid 1) already running
After several hours of googling and after trying lots of commands, I found that its easy to remove the entire container as well as images from the server. Hence I removed all containers with docker rm followed by image deletion with docker rmi. Again i have recreated the docker image on my local system (its working here) and transferred to server. Again I tried to run the docker. But faced same issue again.
Unable to find out the cause & solution. Need some help.
first remove ENTRYPOINT from your Dockerfile and just use:
CMD [ "/usr/sbin/httpd", "-X" ]
the warning regarding AH00558 is comming from your configuration and it i complaining about you do not use www.test.com you can ignore that for now and apache will still working. if you want to read more see this
I searched google for an answer for this question but I haven't got the exact answer. I want to install glassfish in Suse linux server. I downloaded glassfish3.sh from oracle but when I run that script, the folder where glassfish is installed is /home/$user/glassfish and I want to change it.
Does someone know how to change the path of glassfish 3.1.1 in ubuntu server? (only terminal)
Thanks!
You downloaded the .sh file. This will always install GlassFish into the user's home directory. In order to install it into different directory it is a little bit more work to do.
Download and unzip the file. For e.g. you want glassfish to be in: /opt/glassfish:
wget http://download.java.net/glassfish/3.1.1/release/glassfish-3.1.1.zip
sudo unzip glassfish-3.1.1.zip -d /opt
That is it. Glassfish is installed and you can start and use it. But don't forget that you did not configure any automatic start up scripts to glassfish start up automatically.
In order to do that, run this command in your shell:
sudo vim /etc/init.d/glassfish
Paste this content: (first make change that is appropriate to you)
#!/bin/bash
GLASSFISH_HOME=/opt/glassfish3
case "$1" in
start)
${GLASSFISH_HOME}/bin/asadmin start-domain domain1
;;
stop)
${GLASSFISH_HOME}/bin/asadmin stop-domain domain1
;;
restart)
${GLASSFISH_HOME}/bin/asadmin stop-domain domain1
${GLASSFISH_HOME}/bin/asadmin start-domain domain1
;;
*)
echo "usage: $0 {start|stop|restart}"
;;
esac
exit 0
The last thing is to make the script executable by running these commands:
sudo chmod 755 /etc/init.d/glassfish
sudo update-rc.d /etc/init.d/glassfish defaults
Now you can start, stop and restart glassfish like this:
sudo /etc/init.d/glassfish start
sudo /etc/init.d/glassfish stop
sudo /etc/init.d/glassfish restart
I have been trying to work with persistent job queues of gearman. When I try to use libdrizzle like-
gearmand -q libdrizzle --libdrizzle-host=127.0.0.1 --libdrizzle-user=gearman --libdrizzle-password=secret --libdrizzle-db=some_db --libdrizzle-table=gearman_queue --libdrizzle-mysql
It gives me error like-
gearmand: unknown option libdrizzle-host
Also a strange thing is that when I do man gearmand it does not have the libdrizzle options. What should I do? I want the persistent queues in mysql. I had tried using gearman_udf_mysql but it did not work too. I have posted the problem. see Where does mysql save the path for gearman mysql udf files?
Gearman must be compiled with libdrizzle/mysql support. You can check if it's been compiled in by running the command gearmand --help or on older versions man gearmand.
If libdrizzle/mysql support is available, you will see the Drizzle/Mysql options in the help. If it's not there, you will need to recompile gearmand. Here are the commands to install Gearman 1.1.12 on Ubuntu 12.04 LTS (tested on a clean Vagrant precise64 box):
vagrant#precise64:~$ sudo apt-get update
vagrant#precise64:~$ sudo apt-get install libboost-all-dev gperf libevent-dev uuid-dev libmysqld-dev
vagrant#precise64:~$ wget https://launchpad.net/gearmand/1.2/1.1.12/+download/gearmand-1.1.12.tar.gz
vagrant#precise64:~$ tar zxvf gearmand-1.1.12.tar.gz
vagrant#precise64:~$ cd gearmand-1.1.12/
vagrant#precise64:~/gearmand-1.1.12$ ./configure
At this point, look for the following lines at the end of the ./configure output, which indicates Mysql support is installed:
* Building with libdrizzle yes
* Building with libmysql yes
Then continue with the installation:
vagrant#precise64:~/gearmand-1.1.12$ make
vagrant#precise64:~/gearmand-1.1.12$ sudo make install
Gearmand is now configured with libdrizzle and will store jobs in a Mysql database.
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