I would like to try scidb as a replacement for hdf5. I would like to test it on my Debian laptop (no clusters) to give it a try.
Is this possible? Might be that Debian (as opposed to Ubuntu) is not supported?
I had no luck with the installation instructions. The deployment script tells that my OS is not supported. The scidb userguide says about some pre-built packages (for Ubuntu, at least). But there is no hint on how to obtain them.
SciDB is limited to RedHat / CentOS, and to Ubuntu as of the 14.9 release. Folk who want to run it on other distros generally compile from code.
Information about how to obtain the sources (as well as current documentation and community discussion) can be found on the forums here ... http://www.scidb.org/forum/. You'll need to register as a forum user.
Specifically, have a look at http://www.scidb.org/forum/viewtopic.php?f=16&t=364. There's a list of releases and links to code bundles there.
I installed SciDB several times using several ways (building from sources and installing from packages, installing the cluster version and the dev version).
Installation from packages
First, if you choose to install from packages (the easiest and fastest way), SciDB is very very sensitive about your Linux version. For example, for the last version of SciDB (14.8), if you choose to install on a Ubuntu, it has to be a Ubuntu 12.04 (and not a 14.04, a common mistake) 64 bits (meaning you have to install the AMD64 version even if you have an Intel processor). It won't work if you have a different version.
If you have an Ubuntu 12.04 AMD64, Paradigm4 provides a deployment script and a documentation with very simple steps:
https://github.com/Paradigm4/deployment
Installation from sources
It's not so difficult but it can be painful and time consuming. I did it because we had to compile a custom plugin for SciDB. You have two types of installation: dev install (in SciDB user directory) and cluster install (in /opt/ directory).
You have to be registered on their forum to have the link to the source code. They provide a specific documentation to build from source.
Good luck.
Several months ago I have dealt with porting SciDB 14.12 to an unsupported Linux - Fedora 19. If your OS is not supported, it will neither be supported if you try to install from the sources. You have to start from the sources, but then you have to adapt the deployment and installation scripts. The sources can be downloaded from SciDB forum.
Namely, add a new platform to deployment/common/os_detect.sh. Then, there are multiple platform specific deployment scripts, such as deployment/common/prepare_toolchain.sh, deployment/common/prepare_coordinator.sh and deployment/common/prepare_chroot.sh. You need to make sure those prepare the environment as they would on the supported OS'. I used Red Hat 6 and CentOS 6 as a reference, as those are both more similar to Fedora. Since your OS is Debian, you can first try falling back to Ubuntu deployment (in os_detect.sh).
Another problem you may encounter are the 3rd party tools, specially Boost. In my case, I had to build it manually from sources.
Sometimes when porting and debugging it is not convenient to run the scripts with deploy.sh, but it's better to run the deployment scripts directly on the target machine (e.g. coordinator).
Probably the best way to install and to start with SciDB is to download a standard image. With this image you only have to import the virtual machine with a software to virtualize. Moreover there are some characteristics of this virtual machine that are great to develop your first applications.
The main advantage, is that you have an API to SciDB queries and another to R. Then you can explore all options and to test SciDB.
This is the version that I downloaded few months ago: http://www.paradigm4.com/forum/viewtopic.php?f=14&t=1329&sid=606f614e401900cfa750375ba56de656
Nevertheless, there is a problem, the community is too poor. There are little people developing with SciDB.
Related
My question is about whether if it would be possible to run a compiled perl 5.28.0 from source (with GCC 4.8.5 on CentOS 7) to be able to be used on RHEL 5.5 (Tikanga) where GCC version is lower and so would be the other libs like libc, glibc, etc.
Our production environment is running very old perl version (5.8.8) and due to security concerns, it is under heavy lock down, i.e. most of our servers lack make, gcc and related tools and there is no root access available to anyone
I was wondering if it would be possible to compile perl from source i.e. latest 5.28.0 with GCC 4.8.5 AND try to use this compiled version on our production servers (with GCC 4.8.2).
This will save me tonnes of headaches with slow bureaucracy and I can get going with my project with the new tools.
Have not been able to find any discussion or hint about this subject. Can anyone shed some light?
Thank you in advance.
Update after 2 days:
As it seems Perl 5.28 compiled on RHEL7 does not work on RHEL5.5. You will have to compile it on RHEL5.5 and make it relocatable for further usage on any server.
So I Downloaded the RHEL 5.5 and CentOS5.5 ISOs and ran into bootable iso related issues.
Couldn't make a suitable bootable disk for both rhel 5.5 and centos5.5.
rhel5.5 iso was a single dvd image and upon doing file rhel5.5.iso on command prompt, it showed bootable. tried unebootin, rufous iso creator, dd command and created ISOs and tried all of them one by one, but couldn't get it to show boot menu. tried FAT, NTFS FS while making boot disk. Stuck here now.
Centos5.5 iso came in 8 pieces of 600mb files. Had to create a single iso image out of it and found some online procedure to do it and made one ISO file. Got boot menu and looked like it worked. But then it got hung up on doing some sort of source media check test and couldn't proceed further. Found a fix related article that you imprint md5sum on iso and it should work but it didn't.
Just now found something on grokbase and it mentions a new technique, that could take me forward from the point of failure mentioned in point no.3 above.
Edit: static compilation bypasses the problems you are cautious about. You need to figure out whether the result is suitable for your intended purposes.
Otherwise you contend with traditional compilation like you had planned. If the libc is too different, it won't work. You could certainly just go ahead and try, then you'll know for certain.
The real solution is to set up a copy of your production environment (can be in a virtual machine) and compile stuff there.
You could try PerlApp + ActivePerl from ActiveState.com (maybe a part of PDK, Perl Development Kit). I've used it for many years. It compiles perl source and include modules (compiled modules also) into a .exe-program file on Windows and a binary executable file on Linux. There is a payed version and a free/demo version. The payed version allows for cross-compilation and more versions of Perl if I remember correctly.
You might run into trouble with differing versions of glibc/libc on dev vs prod computer, so try to use PerlApp on a CentOS 5.5 Linux (free) for compilation. CentOS5.5 resembles RHEL5.5 enough for most projects. Good luck.
Try perlbrew (is an admin-free perl installation management tool)
I could find that vs2015 comes with mussel library which is more like to use POSIX calls. I went through the installation guide provided and through the official link, came to know that I need to run configuration file followed by make.
But the configuration file has not been provided with vs2015.
I request you to let me know the procedure if someone has done this before.
musl doesn't support Windows; from the FAQ page:
What are musl’s dependencies?
Linux 2.6 or later. Earlier versions will suffice for running most simple single-threaded programs, but due to bugs and conformance issues at the kernel level, musl is not offically supported on earlier kernels.
(now, Windows 10 does support running Linux binaries through WSL, but in that case you would be building musl through gcc inside the Linux "container" and it would be another kind of game entirely)
As it comes as VS2015 along with third party license I thought there should be a way to get it done. The folder location is Microsoft Visual Studio 14.0\VC\vcpackages\IntelliSense\iOS\OSS\musl-1.1.10
As said in the comment, from the folder name it seems that it's there just to aid IntelliSense when editing code for iOS targets.
I need to do a installation of windows updates (OS and Microsoft Security Essentials) on multiple clients using Cent-OS Server. I'm not very familiar with Linux systems and I cant find an appropriate tutorial On the internet.
Give OPSI a try, this is an OpenSource Deployment Solution which works on CentOS:
http://www.opsi.org/
This is an integrated system to deploy full installation as well as simple updates or rollouts.
yum installs RedHat/CentOS/Fedora RPM packages on RedHat/CentOS/Fedora systems. It doesn't have anything to do with Windows. It doesn't understand exe files or anything like that.
I'm not even sure where to begin to understand what the question you are actually trying to ask is... unless your question is really just as confused as it sounds and you are failing to understand the difference between package managed linux systems and Windows systems.
I have a bit of a problem. I need to use the strace utility to figure out why a command is crashing on an older Linux system. Unfortunately, I don't have strace nor do I have gcc/binutils on that system.
I tried building the app statically on a current Debian system, but calls to getpwnam require a dynamic load of the version of libc that was used at compile time. That would be fine, but being that the utilities on the older system were all built using an ancient version of libc, putting a newer libc on that system breaks everything else.
Short of downloading and installing an old distribution of Linux and then doing the build, is there an easier way around this problem? The original distribution on this system is currently unknown and the more I research it, it's getting to seem like a huge chicken vs egg problem. Any tips would be much appreciated.
Using an outdated Linux system is never wise... can it be upgraded? If not, why not? What is failing, and how? Any chance of updating that?
There should be a file named /etc/release or similar, that should give you an idea of the distribution and version. Or uname -a might give a clue on the distribution. If it doesn't work, try to see if commands like rpm, apt-get, or one of the other package management commands are available, that will narrow down the distribution. A Google search for some of the installed packages with versions might help narrow down the version of the distribution.
Knowing distribution and version you may be able to get strace (and perhaps other needed packages). Many distributions keep archival versions (at least of the original installation media for old versions) around.
I apologize in advance for the stupidity of this question, but I am confused as h#&! and not even sure what to ask anymore.
For my math thesis - i.e., I am not a programmer - I have to write C code which uses the CVODE library, which is part of SUNDIALS (do you need all that detail?). But I can't work directly on the Gentoo Linux cluster where the proram will ultimately run.
According to the SUNDIALS' website, CVODE has very rarely been compiled and used in a native Windows environment, but it has been used using Cygwin. So I want to set up a C programming environment, including an IDE (especially a debugger), on my Windows PC, using Cygwin.
I have installed and executed the basic Cygwin (plus a package for nano editor) on my 64-bit Windows PC. I want to use Eclipse IDE, which is available for Linux and Windows, and can really only be used in a graphical interface (I think). I think I should set Eclipse up next (and then CVODE after that). That's what I'm trying to do now.
My basic question is how do I setup Eclipse to work with Cygwin? What Cygwin packages do I need to run Eclipse?
From the docs, I see that Cygwin has a server (Cygserver), but does not have a graphical interface. Or, it might have a graphical interface called Cygwin/X. Do I setup Eclipse in Windows to communicate with Cygserver, then do my work in Windows, but compilations and so forth would take place in the Cygserver? Or, do I install Cygwin/X and use a Linux version of Eclipse which, hopefully, works with Cygwin/X? If both are possible options, which is easier (I'm guessing the latter).
Cygwin is nice but I've run into issues now and then with it. I would recommend that you download Virtualbox or some similar VM software and install the same Linux that is there on your production cluster inside it. Then you'll have an environment on your development machine which matches the production one.
Now, install eclipse (and anything else you want) inside the VM and you can develop the software there smoothly without worrying about tangential issues like cygwin and the rest.