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

Fenoy Gerald gerald.fenoy at geolabs.fr
Fri Jan 8 03:30:09 PST 2016 

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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