[Zoo-discuss] Zoo-project installation and running on Centos-6

Fenoy Gerald gerald.fenoy at geolabs.fr
Fri Jan 8 23:42:26 PST 2016 

Dear Francesco,
thanks for your confirmation.

The documentation has been updated consequently.

Best regards,

> Le 8 janv. 2016 à 18:20, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
> 
> Dear Gerald,
> 
> thank you very much for the hint.
> 
> I confirm you that this fixes all the runtime errors I had with java also with different jvm versions.
> 
> Best regards,
> 
> Francesco.
> 
> On 08/gen/2016, at 11:30, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
> 
>> Dear Francesco,
>> let's focus on the java-1.7.0-openjdk case first, can you try to add the following to your main.cfg and confirm that it solves your problem ?
>> 
>> [javax]
>> ss=2m
>> 
>> 
>> Best regards,
>> 
>> 
>>> Le 7 janv. 2016 à 18:44, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
>>> 
>>> Dear Gerald,
>>> thanks for updating and validating a new procedure.
>>> 
>>> I’m trying to follow it and the installation phase comes more smooth now.
>>> 
>>> Unfortunately I still cannot run the HelloWorldJava service.
>>> This is what I get if I use  java-1.7.0-openjdk (and later versions):
>>> 
>>> ./zoo_loader.cgi "Service=WPS&Request=Execute&Version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=myName"
>>> Error occurred during initialization of VM
>>> java.lang.StackOverflowError
>>> 	at java.lang.Object.<clinit>(Object.java:41)
>>> 
>>> If I use a 1.6.0 version of libjvm.so I get:
>>> 
>>> ./zoo_loader.cgi "Service=WPS&Request=Execute&Version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=myName"
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <ows:ExceptionReport xmlns:ows="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd" xml:lang="en-US" version="1.1.0">
>>> <ows:Exception exceptionCode="InternalError">
>>>  <ows:ExceptionText>ZOO Kernel failed to process your request, receiving signal 11 = SIGSEGV</ows:ExceptionText>
>>> </ows:Exception>
>>> </ows:ExceptionReport>
>>> 
>>> Can you figure out what is the problem here?
>>> 
>>> Thanks in advance,
>>> 
>>> Francesco.
>>> 
>>> On 05/gen/2016, at 08:08, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
>>> 
>>>> Dear Francesco,
>>>> I do apologize for answering so late.
>>>> 
>>>> After you send this email, I’ve setup a fresh CentOS 6 and used the following setup procedure :
>>>> 
>>>> rpm -Uvh http://elgis.argeo.org/repos/6/elgis-release-6-6_0.noarch.rpm
>>>> rpm -Uvh \
>>>> http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
>>>> wget\
>>>> http://proj.badc.rl.ac.uk/cedaservices/raw-attachment/ticket/670/armadillo-3.800.2-1.el6.x86_64.rpm
>>>> yum install armadillo-3.800.2-1.el6.x86_64.rpm
>>>> yum install hdf5.so.6
>>>> yum install gcc-c++ zlib-devel libxml2-devel bison openssl \
>>>> python-devel subversion libxslt-devel libcurl-devel \
>>>> gdal-devel proj-devel libuuid-devel openssl-devel fcgi-devel
>>>> yum install java-1.7.0-openjdk-devel
>>>> 
>>>> Then I make sure tu use correct version of both java and java using the update-alternatives --config java and update-alternatives --config java commands
>>>> 
>>>> Everything now works well for the Java support on this platform. There were few mistakes which was fixed on the way inside the ZOO-Project Java support which did not appear when using this support on MacOS X.
>>>> 
>>>> I have jus updated the installation documentation for CentOS and I thank you for your comment and your help for this.
>>>> 
>>>> Best regards,
>>>> 
>>>>> Le 18 déc. 2015 à 18:55, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
>>>>> 
>>>>> Dear Gerald,
>>>>> 
>>>>> thank you for the quick response.
>>>>> 
>>>>>> For the parameters you added to your httpd.conf for LD_LIBRARY_PATH, I think it is not required. Nevertheless, you should need to run ldconfig after you setup your ZOO-Kernel (by running make install). This should probably solve your issue with GetCapabilities and DescribeProcess.
>>>>> 
>>>>> as you can see from the procedure I’ve described, I did the make install but it wasn’t enough.
>>>>> 
>>>>>> For the issue when trying to Execute a Java service, I supposed that the issue came because you did not setup the ZOO-API Java Class. 
>>>>> 
>>>>> Sorry to have missed this in the previous email. I’ve compiled and copied the ZOO-API Java Class but nothing has changed. This is the content of my cgi environment:
>>>>> 
>>>>> -rw-r--r-- 1 root root   1527 Dec 17 16:30 HelloJava.class
>>>>> -rwxr-xr-x 1 root root    691 Dec 18 12:43 HelloWorldJava.zcfg
>>>>> -rwxr-xr-x 1 root root  48038 Dec 17 15:29 libZOO.so
>>>>> -rw-r--r-- 1 root root    759 Dec 17 16:05 main.cfg
>>>>> -rw-r--r-- 1 root root   1580 Dec 17 16:35 test_service.py
>>>>> -rw-r--r-- 1 root root    840 Dec 17 16:43 test_service.pyc
>>>>> -rw-r--r-- 1 root root    648 Dec 17 15:29 ZOO.class
>>>>> -rwxr-xr-x 1 root root 445354 Dec 17 16:05 zoo_loader.cgi
>>>>> 
>>>>>> Maybe it can help me if you can provide the back trace from gdb after the segfault.
>>>>> 
>>>>> Here is the complete backtrace:
>>>>> 
>>>>> (gdb) run "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>>>> Starting program: /var/www/cgi-bin/zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>>>> [Thread debugging using libthread_db enabled]
>>>>> [New Thread 0x7fffe7283700 (LWP 7268)]
>>>>> [New Thread 0x7fffe7182700 (LWP 7269)]
>>>>> [New Thread 0x7fffe6b8b700 (LWP 7270)]
>>>>> 
>>>>> Program received signal SIGSEGV, Segmentation fault.
>>>>> 0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> Missing separate debuginfos, use: debuginfo-install libidn-1.18-2.el6.x86_64
>>>>> (gdb) bt
>>>>> #0  0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #1  0x00007ffff51d6acf in java_lang_Throwable::fill_in_stack_trace(Handle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #2  0x00007ffff51d6b79 in java_lang_Throwable::fill_in_stack_trace(Handle) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #3  0x00007ffff5126d67 in Exceptions::throw_stack_overflow_exception(Thread*, char const*, int) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #4  0x00007ffff51d04e1 in JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) ()
>>>>> from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #5  0x00007ffff5400869 in os::os_exception_wrapper(void (*)(JavaValue*, methodHandle*, JavaCallArguments*, Thread*), JavaValue*, methodHandle*, JavaCallArguments*, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #6  0x00007ffff51d03b5 in JavaCalls::call(JavaValue*, methodHandle, JavaCallArguments*, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #7  0x00007ffff519ffb5 in instanceKlass::call_class_initializer_impl(instanceKlassHandle, Thread*) ()
>>>>> from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #8  0x00007ffff519e538 in instanceKlass::initialize_impl(instanceKlassHandle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #9  0x00007ffff519d8fa in instanceKlass::initialize(Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #10 0x00007ffff519e7fc in instanceKlass::initialize_impl(instanceKlassHandle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #11 0x00007ffff519d8fa in instanceKlass::initialize(Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #12 0x00007ffff550f654 in Threads::create_vm(JavaVMInitArgs*, bool*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #13 0x00007ffff520b790 in JNI_CreateJavaVM () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>> #14 0x000000000040ceb4 in zoo_java_support ()
>>>>> #15 0x0000000000406fa3 in loadServiceAndRun (myMap=0x7fffffffe188, s1=0x65d0b0, request_inputs=0x65be20, inputs=<value optimized out>, ioutputs=
>>>>> 0x7fffffffe178, eres=0x7fffffffe19c) at zoo_service_loader.c:622
>>>>> #16 0x00000000004090c6 in runRequest (inputs=<value optimized out>) at zoo_service_loader.c:2141
>>>>> #17 0x000000000040628a in cgiMain () at zoo_loader.c:402
>>>>> #18 0x000000000042b63f in main (argc=2, argv=0x7fffffffe458) at cgic.c:312
>>>>> 
>>>>> 
>>>>> Best regards,
>>>>> 
>>>>> Francesco.
>>>>> 
>>>>> On 18/dic/2015, at 11:32, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
>>>>> 
>>>>>> Hello Francesco,
>>>>>> nice to hear that you are willing to adopt the ZOO-Project.
>>>>>> 
>>>>>> First of all, I have to say that this documentation has been written 5 years ago, so any help on setting up the ZOO-Project on CentOS is probably needed. The original version was there : [1].
>>>>>> 
>>>>>> For the package names I have to admit that I don’t have access to any CentOS host to verify the package names, so the correct names will help us to fix this part of the documentation.
>>>>>> 
>>>>>> For the parameters you added to your httpd.conf for LD_LIBRARY_PATH, I think it is not required. Nevertheless, you should need to run ldconfig after you setup your ZOO-Kernel (by running make install). This should probably solve your issue with GetCapabilities and DescribeProcess.
>>>>>> 
>>>>>> I suppose that there is no need anymore for removing any line from ulinet.c to get it working. I hope you can confirm this by executing services passing parameter by reference rather than by value.
>>>>>> 
>>>>>> For the issue when trying to Execute a Java service, I supposed that the issue came because you did not setup the ZOO-API Java Class. So I tried it locally but I have a standard Exception report returned in this case and it contains the following information: * Exception in thread "main" java.lang.NoClassDefFoundError: ZOO * . So there should be no problem here. Maybe it can help me if you can provide the back trace from gdb after the segfault.
>>>>>> 
>>>>>> I hope to hear back from you,
>>>>>> Best regards,
>>>>>> 
>>>>>> [1] http://zoo-project.org/trac/wiki/ZooDocumentation/ZOOKernel/CentOS_installation 
>>>>>> 
>>>>>> 
>>>>>>> Le 18 déc. 2015 à 10:47, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
>>>>>>> 
>>>>>>> Hello!
>>>>>>> 
>>>>>>> In the context of our Earth Observation projects my company (Terradue UK) would like to adopt your implementation of WPS, .
>>>>>>> 
>>>>>>> The typical environment where to install the server is a VM with CentOS release 6.7 x86_64 .
>>>>>>> 
>>>>>>> INSTALLATION:
>>>>>>> 
>>>>>>> From the official documentation:
>>>>>>> 
>>>>>>> http://zoo-project.org/docs/install/centos.html
>>>>>>> 
>>>>>>> If I've tried to follow the list of commands I quickly found some issue or incorrect steps:
>>>>>>> 
>>>>>>> yum install apache2
>>>>>>> do you mean httpd?
>>>>>>> yum install build-essentials
>>>>>>> do you mean yum groupinstall "Development Tools” ?
>>>>>>> yum install gcc-c++ 
>>>>>>> yum install libxml2-devel 
>>>>>>> yum install zlib-devel 
>>>>>>> yum install bison 
>>>>>>> yum install openssl   
>>>>>>> yum install python-devel
>>>>>>> yum install subversion 
>>>>>>> 
>>>>>>> Additional prerequisites found:
>>>>>>> 
>>>>>>> yum install libxslt-devel.x86_64 
>>>>>>> yum install libcurl-devel 
>>>>>>> yum install gdal-devel 
>>>>>>> yum install proj-devel.x86_64 
>>>>>>> yum install libuuid-devel
>>>>>>> yum install openssl-devel
>>>>>>> 
>>>>>>> FOR GDAL 1.8.0 (otherwise zoo-kernel will complain about VSILFILE)
>>>>>>> 
>>>>>>> wget http://download.osgeo.org/gdal/gdal-1.8.0.tar.gz
>>>>>>> tar xzf gdal-1.8.0.tar.gz
>>>>>>> cd gdal-1.8.0
>>>>>>> ./configure  # add your options here
>>>>>>> make
>>>>>>> make install
>>>>>>> 
>>>>>>> TO INSTALL FASTCGI
>>>>>>> 
>>>>>>> wget http://www.fastcgi.com/dist/fcgi.tar.gz
>>>>>>> tar xzf fcgi.tar.gz
>>>>>>> cd fcgi-2.4.1-SNAP-0311112127/	
>>>>>>> 
>>>>>>> PATCH (from http://stackoverflow.com/questions/4577453/fcgio-cpp50-error-eof-was-not-declared-in-this-scope):
>>>>>>> 
>>>>>>> 	--- include/fcgio.h 2012-01-23 15:23:51.136063795 +0000
>>>>>>> 	+++ include/fcgio.h 2012-01-23 15:22:19.057221383 +0000
>>>>>>> 	@@ -31,6 +31,7 @@
>>>>>>> 	#define FCGIO_H
>>>>>>> 
>>>>>>> 	 #include <iostream>
>>>>>>> 	+#include <stdio.h>
>>>>>>> 
>>>>>>> 	 #include "fcgiapp.h"
>>>>>>> 
>>>>>>> ./configure
>>>>>>> make
>>>>>>> make install
>>>>>>> echo /usr/local/lib >> /etc/ld.so.conf.d/local.conf
>>>>>>> ldconfig
>>>>>>> 
>>>>>>> TO INSTALL autoconf tools (OK)
>>>>>>> 
>>>>>>> TO INSTALL FLEX TOOL (OK)
>>>>>>> 
>>>>>>> CURL:
>>>>>>> 
>>>>>>> To avoid the installation of a different version of Curl, I want to follow the guide about changing the file ulinet.c but the link to the code is broken and:
>>>>>>> 
>>>>>>> line 173 is :
>>>>>>> 
>>>>>>> printf("\n**[PROXY SETTINGS DETECTION %s (%d) %s:%li (%s)]**\n",proto,proxy_enabled,(char*)proxy_host,proxy_port,buffer);
>>>>>>> 
>>>>>>> line 175 is a white line
>>>>>>> 
>>>>>>> Should I comment these lines?
>>>>>>> 
>>>>>>> Anyway our base line version is 7.19.7. Is it good?
>>>>>>> 
>>>>>>> INSTALL ZOO-KERNEL 
>>>>>>> Since this section is totally missing I got inspiration from the previous version (still incomplete and not working):
>>>>>>> 
>>>>>>> http://www.zoo-project.org/docs/kernel/install-centos.html
>>>>>>> 
>>>>>>> svn co http://svn.zoo-project.org/svn/trunk zoo-project
>>>>>>> cd zoo-project/thirds/cgic206
>>>>>>> edit file Makefile in order to set the current fgci path adding:
>>>>>>> 	LIBS= -L./ -lcgic /usr/local/lib/libfcgi.so
>>>>>>> make 
>>>>>>> cd ../../zoo-project/zoo-kernel
>>>>>>> autoconf
>>>>>>> ./configure --with-java=/usr/java/jdk1.6.0_35/ --with-python --with-gdal_config=/usr/bin/gdal-config
>>>>>>> make zoo_loader.cgi
>>>>>>> make install
>>>>>>> cp main.cfg /var/www/cgi-bin/
>>>>>>> cp zoo_loader.cgi /var/www/cgi-bin/
>>>>>>> 
>>>>>>> In httpd.conf I have to add:
>>>>>>> SetEnv LD_LIBRARY_PATH /usr/local/lib/
>>>>>>> 
>>>>>>> Now the GetCapabilities and DescribeProcess calls work fine.
>>>>>>> 
>>>>>>> EXECUTE:
>>>>>>> 
>>>>>>> HelloPy works fine.
>>>>>>> 
>>>>>>> HelloWorldJava is not working:
>>>>>>> 
>>>>>>> From the Browser => 500 Internal Server Error
>>>>>>> 
>>>>>>> Form the command line:
>>>>>>> 
>>>>>>> ./zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"Content-Type: text/xml; charset=UTF-8
>>>>>>> Status: 501 Internal Server Error
>>>>>>> 
>>>>>>> Segmentation fault
>>>>>>> 
>>>>>>> 
>>>>>>> With gdb:
>>>>>>> 
>>>>>>> (gdb) run "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>>>>>> Starting program: /var/www/cgi-bin/zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>>>>>> [Thread debugging using libthread_db enabled]
>>>>>>> [New Thread 0x7fffe7283700 (LWP 29445)]
>>>>>>> [New Thread 0x7fffe7182700 (LWP 29446)]
>>>>>>> [New Thread 0x7fffe6b8b700 (LWP 29447)]
>>>>>>> 
>>>>>>> Program received signal SIGSEGV, Segmentation fault.
>>>>>>> 0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>>>>>> 
>>>>>>> 
>>>>>>> CONCLUSIONS
>>>>>>> 
>>>>>>> I hope that my experience could help you to improve the installation procedure description and I hope you could help me to find out the reason of the failed execution.
>>>>>>> 
>>>>>>> Best Regards,
>>>>>>> 
>>>>>>> Francesco Barchetta
>>>>>>> 
>>>>>>> Terradue UK
>>>>>>> _______________________________________________
>>>>>>> Zoo-discuss mailing list
>>>>>>> Zoo-discuss at lists.osgeo.org
>>>>>>> http://lists.osgeo.org/mailman/listinfo/zoo-discuss
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Gérald Fenoy
>>>>>> http://wiki.osgeo.org/wiki/User:Djay
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Zoo-discuss mailing list
>>>>> Zoo-discuss at lists.osgeo.org
>>>>> http://lists.osgeo.org/mailman/listinfo/zoo-discuss
>>>> 
>>>> 
>>>> 
>>>> Gérald Fenoy
>>>> http://wiki.osgeo.org/wiki/User:Djay
>>>> 
>>> 
>> 
>> 
>> 
>> Gérald Fenoy
>> http://wiki.osgeo.org/wiki/User:Djay
>> 
> 
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Gérald Fenoy
http://wiki.osgeo.org/wiki/User:Djay

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