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<== Date ==> <== Thread ==>

Subject: RE: mcaR7-0
From: Mark Rivers <rivers@cars.uchicago.edu>
To: "'Szalata, Zenon M.'" <zms@slac.stanford.edu>, "tech-talk@aps.anl.gov" <tech-talk@aps.anl.gov>
Date: Wed, 1 Feb 2012 18:43:22 +0000

Hi Zen,

 

This is a known problem with areaDetector R1-7 on older Linux systems.  It is documented in the R1-8 release notes:

 

  • Support libraries. The static Linux support libraries provided in R1-7 were built on a Fedora Core 9 system (gcc 4.3.0) for 32-bit linux-x86, and on a Fedora Core 14 system (gcc 4.5.1) for 64-bit linux-x86_64. Problems arose when trying to build with these libraries or to run the pre-built binaries on older Linux systems, e.g. those with gcc 4.1.2. These were fixed as follows:
    • The Prosilica libPvAPI.a file had been taken from the AVT gcc 4.3 directory. This was replaced with the one from the gcc 4.1 directory because the 4.3 version requires a newer version of GLIBCXX.
    • The HDF5 library had been built with the default -std=c99. This caused the function isoc99_sscanf() to be called instead of sscanf(), and the former function does not exist on older Linux systems. The HDF library was rebuilt with -std=gnu89 on 32-bit and 64-bit Linux.
    • libGraphicsMagic++.a on 64-bit was invoking std::_List_mode_base functions that do not exist in earlier versions of GLIBCXX. GraphicsMagick was rebuilt on an older Linux system (gcc 4.2.1) for 64-bit Linux.
    • All of the prebuilt 64-bit binaries were recompiled and relinked on an older Linux system (gcc 4.2.1).

 

R1-8 has not been released yet, but R1-8beta1 has been released, and it fixes this problem.

 

Mark

 

 

-----Original Message-----
From: Szalata, Zenon M. [mailto:zms@slac.stanford.edu]
Sent: Wednesday, February 01, 2012 12:11 PM
To: Mark Rivers; tech-talk@aps.anl.gov
Subject: RE: mcaR7-0

 

Hi Mark,

I should have remembered that.

 

So now I am building area detector on RHEL6 64bit Linux and I am getting this link error:

 

/usr/bin/g++ -c  -D_POSIX_C_SOURCE=199506L -D_POSIX_THREADS -D_XOPEN_SOURCE=500           -D_X86_64_  -DUNIX  -D_BSD_SOURCE -Dlinux  -D_REENTRANT   -g   -Wall      -m64      -MMD -I. -I../O.Common -I. -I.. -I../../../include/os/Linux -I../../../include      -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/asyn/R4.18/include  -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/calc/R2.9/include  -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/busy/R1.4/include  -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/sscan/R2.7/include  -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/mca/R7.0/include -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/include/os/Linux -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/include -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/include/os/Linux -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/include -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/include/os/Linux -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/include       ../simDetectorAppMain.cpp

/usr/bin/g++ -o simDetectorApp -Wl,-Bstatic -L/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/asyn/R4.18/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/busy/R1.4/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/calc/R2.9/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/mca/R7.0/lib/linux-x86_64 -L/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/sscan/R2.7/lib/linux-x86_64 -Wl,-rpath,/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/asyn/R4.18/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/busy/R1.4/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/calc/R2.9/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/mca/R7.0/lib/linux-x86_64 -Wl,-rpath,/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/sscan/R2.7/lib/linux-x86_64       -m64                simDetectorApp_registerRecordDeviceDriver.o simDetectorAppMain.o   -lsimDetector -lNDPlugin -lADBase -lnetCDF -lcalc -lbusy -lsscan -lautosave -lmca -lasyn -lrecIoc -lsoftDevIoc -lmiscIoc -lrsrvIoc -ldbtoolsIoc -lasIoc -ldbIoc -lregistryIoc -ldbStaticIoc -lca -lCom -lPvAPI -lGraphicsMagick++ -lGraphicsMagickWand -lGraphicsMagick -lNeXus -lhdf5 -lsz -ltiff -ljpeg -lz -Wl,-Bdynamic -lgomp -lX11 -lxml2 -lpng12 -lbz2 -lXext -lfreetype -lpthread   -lreadline -lncurses -lm -lrt -ldl -lgcc

/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64/libGraphicsMagick++.a(Drawable.o): In function `std::list<Magick::Coordinate, std::allocator<Magick::Coordinate> >::_M_insert(std::_List_iterator<Magick::Coordinate>, Magick::Coordinate const&)':

Drawable.cpp:(.text._ZNSt4listIN6Magick10CoordinateESaIS1_EE9_M_insertESt14_List_iteratorIS1_ERKS1_[std::list<Magick::Coordinate, std::allocator<Magick::Coordinate> >::_M_insert(std::_List_iterator<Magick::Coordinate>, Magick::Coordinate const&)]+0x3a): undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)'

/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64/libGraphicsMagick++.a(Drawable.o): In function `std::list<Magick::VPath, std::allocator<Magick::VPath> >::_M_insert(std::_List_iterator<Magick::VPath>, Magick::VPath const&)':

Drawable.cpp:(.text._ZNSt4listIN6Magick5VPathESaIS1_EE9_M_insertESt14_List_iteratorIS1_ERKS1_[std::list<Magick::VPath, std::allocator<Magick::VPath> >::_M_insert(std::_List_iterator<Magick::VPath>, Magick::VPath const&)]+0x3a): undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)'

/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64/libGraphicsMagick++.a(Drawable.o): In function `std::list<Magick::PathArcArgs, std::allocator<Magick::PathArcArgs> >::_M_insert(std::_List_iterator<Magick::PathArcArgs>, Magick::PathArcArgs const&)':

Drawable.cpp:(.text._ZNSt4listIN6Magick11PathArcArgsESaIS1_EE9_M_insertESt14_List_iteratorIS1_ERKS1_[std::list<Magick::PathArcArgs, std::allocator<Magick::PathArcArgs> >::_M_insert(std::_List_iterator<Magick::PathArcArgs>, Magick::PathArcArgs const&)]+0x3a): undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)'

/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64/libGraphicsMagick++.a(Drawable.o): In function `std::list<Magick::PathCurvetoArgs, std::allocator<Magick::PathCurvetoArgs> >::_M_insert(std::_List_iterator<Magick::PathCurvetoArgs>, Magick::PathCurvetoArgs const&)':

Drawable.cpp:(.text._ZNSt4listIN6Magick15PathCurvetoArgsESaIS1_EE9_M_insertESt14_List_iteratorIS1_ERKS1_[std::list<Magick::PathCurvetoArgs, std::allocator<Magick::PathCurvetoArgs> >::_M_insert(std::_List_iterator<Magick::PathCurvetoArgs>, Magick::PathCurvetoArgs const&)]+0x3a): undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)'

/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/lib/linux-x86_64/libGraphicsMagick++.a(Drawable.o): In function `std::list<Magick::PathQuadraticCurvetoArgs, std::allocator<Magick::PathQuadraticCurvetoArgs> >::_M_insert(std::_List_iterator<Magick::PathQuadraticCurvetoArgs>, Magick::PathQuadraticCurvetoArgs const&)':

Drawable.cpp:(.text._ZNSt4listIN6Magick24PathQuadraticCurvetoArgsESaIS1_EE9_M_insertESt14_List_iteratorIS1_ERKS1_[std::list<Magick::PathQuadraticCurvetoArgs, std::allocator<Magick::PathQuadraticCurvetoArgs> >::_M_insert(std::_List_iterator<Magick::PathQuadraticCurvetoArgs>, Magick::PathQuadraticCurvetoArgs const&)]+0x3a): undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)'

collect2: ld returned 1 exit status

make[3]: *** [simDetectorApp] Error 1

make[3]: Leaving directory `/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/ADApp/simDetectorSrc/O.linux-x86_64'

make[2]: *** [install.linux-x86_64] Error 2

make[2]: Leaving directory `/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/ADApp/simDetectorSrc'

make[1]: *** [simDetectorSrc.install] Error 2

make[1]: Leaving directory `/afs/slac.stanford.edu/g/testfac/vol1/rhel6/epics/R3.14.12.2/modules/areaD/R1.7/ADApp'

make: *** [ADApp.install] Error 2

 

I modified ADApp/Makefile to build only a few components.  Here is my Makefile:

 

zms@ilc-esb09 $ less Makefile

TOP = ..

include $(TOP)/configure/CONFIG

 

DIRS += ADSrc

DIRS += netCDFSrc

DIRS += cbfSrc

# prosilicaSupport must be built before pluginSrc or prosilicaSrc because it installs

# header and library files needed by both

DIRS += prosilicaSupport

DIRS += tiffSupport

DIRS += hdf5Support

DIRS += nexusSrc

DIRS += pvcamSupport

DIRS += magickSupport

DIRS += pluginSrc

pluginSrc_DEPEND_DIRS = ADSrc netCDFSrc prosilicaSupport tiffSupport hdf5Support nexusSrc magickSupport

DIRS += simDetectorSrc

simDetectorSrc_DEPEND_DIRS = pluginSrc

DIRS += URLSrc

URLSrc_DEPEND_DIRS = pluginSrc

DIRS += prosilicaSrc

prosilicaSrc_DEPEND_DIRS = pluginSrc

#DIRS += pilatusSrc

#pilatusSrc_DEPEND_DIRS   = pluginSrc cbfSrc

#DIRS += marCCDSrc

#marCCDSrc_DEPEND_DIRS = pluginSrc

#DIRS += mar345Src

#mar345Src_DEPEND_DIRS = pluginSrc

#DIRS += adscSrc

#adscSrc_DEPEND_DIRS = pluginSrc

#DIRS += roperSrc

#roperSrc_DEPEND_DIRS = pluginSrc

#DIRS += firewireWinSrc

#firewireWinSrc_DEPEND_DIRS = pluginSrc

#DIRS += perkinElmerSrc

#perkinElmerSrc_DEPEND_DIRS = pluginSrc

#DIRS += pvcamSrc

#pvcamSrc_DEPEND_DIRS = pluginSrc pvcamSupport

#DIRS += brukerSrc

#brukerSrc_DEPEND_DIRS = pluginSrc

#DIRS += PSLSrc

#PSLSrc_DEPEND_DIRS = pluginSrc

DIRS := $(DIRS) $(filter-out $(DIRS), $(wildcard *db*))

DIRS := $(DIRS) $(filter-out $(DIRS), $(wildcard *Db*))

include $(TOP)/configure/RULES_DIRS

 

 

 

> -----Original Message-----

> From: Mark Rivers [mailto:rivers@cars.uchicago.edu]

> Sent: Tuesday, January 31, 2012 6:41 PM

> To: Szalata, Zenon M.; tech-talk@aps.anl.gov

> Subject: RE: mcaR7-0

>

>

> Hi Zen,

>

> The CanberraSrc directory in mcaApp is failing because you don't have libnet

> and libpcap installed on that system.

>

> Here are 3 choices.  Any one of them should fix your problem.

>

> 1) Install libnet and libpcap.  I would only recommend doing this if you want to

> use the Canberra mca modules.

>

> 2) If you are building using the top-level synApps files then in

> $(SUPPORT)/configure/CONFIG_SITE you will find these lines:

>

> #Set the following variable to YES if libnet has been installled

> #on the host Linux system for the MCA support module, otherwise,

> #set to NO.

> LINUX_NET_INSTALLED = YES

> export LINUX_NET_INSTALLED

>

> Change YES to NO and rebuild.

>

> You could also put that in mca/configure/CONFIG_SITE

>

> 3) In mcaApp/Makefile comment out the line to build CanberraSrc

>

> Cheers,

> Mark

>

>

>

>

>

> *************************************************************

> *******************************

>

> From: Szalata, Zenon M. [zms@slac.stanford.edu]

>

> Sent: Tuesday, January 31, 2012 7:58 PM

>

> To: Mark Rivers; tech-talk@aps.anl.gov

>

> Subject: mcaR7-0

>

>

>

> Hi Mark,

> I am failing miserably to build this module on RHEL6 64bit Linux.

> I get a lot of errors, but some of the first are:

>

> /usr/bin/gcc -c  -D_POSIX_C_SOURCE=199506L -D_POSIX_THREADS -

> D_XOPEN_SOURCE=500           -D_X86_64_  -DUNIX  -D_BSD_SOURCE -Dlinux  -

> D_REENTRANT   -g   -Wall     -DUSE_LIBNET -g `libnet-config

>  --defines`   -m64     -fPIC -MMD -I. -I../O.Common -I. -I.. -I../../../include/os/Linux

> -I../../../include      -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/calc/R2.9/include  -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/sscan/R2.7/include

>  -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/busy/R1.4/include     -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/include/os

> /Linux -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/autosave/R4.8/include  -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/asyn/R4.18/include

>  -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/mca/R7.0/include/os/Linu

> x -I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/modules/mca/R7.0/include -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/include/os/Linux -

> I/afs/slac/g/testfac/rhel6/epics/R3.14.12.2/base/include

>  ../nmc_comm_subs_1.c

> /bin/sh: libnet-config: command not found

> In file included from ../nmc_comm_subs_1.c:70:

> ../nmc_sys_defs.h:52:24: warning: libnet.h: No such file or directory

> ../nmc_sys_defs.h:53:22: warning: pcap.h: No such file or directory

> In file included from ../nmc_comm_subs_1.c:70:

> ../nmc_sys_defs.h:158: error: expected specifier-qualifier-list before 'libnet_t'

> ../nmc_sys_defs.h:188: error: expected specifier-qualifier-list before 'pcap_t'

> ../nmc_sys_defs.h:262: warning: 'struct pcap_pkthdr' declared inside

> parameter list

> ../nmc_sys_defs.h:262: warning: its scope is only this definition or declaration,

> which is probably not what you want

> ../nmc_comm_subs_1.c: In function 'nmc_initialize':

> ../nmc_comm_subs_1.c:170: error: 'PCAP_ERRBUF_SIZE' undeclared (first use

> in this function)

> ../nmc_comm_subs_1.c:170: error: (Each undeclared identifier is reported

> only once

> ../nmc_comm_subs_1.c:170: error: for each function it appears in.)

> ../nmc_comm_subs_1.c:171: error: storage size of 'bpfprog' isn't known

> ../nmc_comm_subs_1.c:172: error: 'bpf_u_int32' undeclared (first use in this

> function)

> ../nmc_comm_subs_1.c:172: error: expected ';' before 'netp'

> ../nmc_comm_subs_1.c:323: error: 'struct nmc_comm_info_struct' has no

> member named 'pcap'

> ../nmc_comm_subs_1.c:323: warning: implicit declaration of function

> 'pcap_open_live'

> ../nmc_comm_subs_1.c:327: error: 'struct nmc_comm_info_struct' has no

> member named 'pcap'

> ../nmc_comm_subs_1.c:330: error: 'pcap_if_t' undeclared (first use in this

> function)

> ../nmc_comm_subs_1.c:330: error: 'alldevs' undeclared (first use in this

> function)

> ../nmc_comm_subs_1.c:331: error: 'd' undeclared (first use in this function)

>

> Should I try an earlier version of mca?

>

> Thanks,

> Zen

>

>

>

 


Replies:
RE: mcaR7-0 Szalata, Zenon M.
References:
std_R3_1 Szalata, Zenon M.
RE: std_R3_1 Mark Rivers
mcaR7-0 Szalata, Zenon M.
RE: mcaR7-0 Mark Rivers
RE: mcaR7-0 Szalata, Zenon M.

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