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Abaqus 6.6 on Debian Etch (amd64 port)

Q. Why does the condemned man get a last cigarette, instead of one of those through-the-skin stick-on nicotine thingies?

A. Don’t patch the executable.

rec.humor.funny

Bad Abaqus! Or more properly, bad ZeroG InstallAnywhere! This post indicates that AMD64 Java doesn’t have NPTL problems you keep checking for. And then, when I comment out the parts of the installer script that check for that, it ends up shifting the position of this godawful binary you put at the end of what was otherwise a shell script (or two), and then it won’t extract properly, and I end up searching half the day trying to figure out why I keep getting

Exception in thread "main" java.lang.NoClassDefFoundError: com/zerog/lax/LAX

errors every time I run the installer. So note to anyone else installing Abaqus on amd64 Debian (i386 works fine if you use the -nosystemchecks flag): make sure any line you put a comment on, you either edit in overwrite mode, or you make sure you delete a character for every # sign you add. Example patch section:

--- /cdrom/lnx86_64/product/UNIX/Disk1/InstData/NoVM/install.bin
+++ /tmp/aba/lnx86_64/product/UNIX/Disk1/InstData/NoVM/install.bin
@@ -2086,49 +2086,49 @@
if [ `uname` = "Linux" ]; then
debugOut "checking for NPTL + JVM vulernability..."
#check libc to see if it was compiled with NPTL
-       nptl="`strings /lib/libc.so.6 | grep -i nptl`"
-       if [ "$nptl" ]; then
-               debugOut "NPTL detected! checking for vulnerable JVM....";
+#nptl="`strings /lib/libc.so.6 | grep -i nptl`"
+#if [ "$nptl" ]; then
+#      debugOut "NPTL detected! checking for vulnerable JVM....";

note how each # sign has replaced one tab or other whitespace character. Your ultimate goal here is to convince the installer that you do not, in fact, need any LD_ASSUME_KERNEL hackery here. If you let Abaqus continue with its out-of-the-box amd64 install, all kinds of stuff like ls, nawk, etc. will complain with problems loading shared libraries.

So copy the installation CD to the hard drive, edit install.bin along the lines of what’s shown above, and run the main setup script with the -nosystemchecks flag. You might also want to use -jre system flag as well if you have Sun Java installed.

And on a much less aggravating note, to paraphrase from The Princess Bride: this flag -console, I do not think it means what you think it means:

abaqus-console-install.jpg

{ 21 } Comments

  1. Dimitrios Eftaxiopou | May 10, 2007 at 1:10 am | Permalink

    Hello,
    I have ABAQUS 6.5 on Debian sarge (oldstable) working fine. No Intel compiler installed since I don’t need any external subroutines at the moment.

    I have installed ABAQUS 6.6-5 on Debian testing i386 (lenny), but I cannot make ABAQUS/CAE to work. When I executed the command “abaqus cae” I used to get an error that

    del relFile: relFile not found

    in abaagus6.env file. I commented out this line in abaqus6.env file in the /site directory of the ABAQUS installation tree. Then, I got the error

    libgcc1:version GCC 4_2 not found (required
    by /usr/lib/libstdc++6.so)

    So I copied libgcc1.so from /lib to the /External directory in the ABAQUS tree.

    Then I get the error

    ABAQUS License Manager checked out the following license(s):
    “cae” version 6.6 from 147.102.246.1
    .
    forrtl: info: Fortran error message number is 174.
    forrtl: warning: Could not open message catalog: ifcore_msg.cat.
    forrtl: info: Check environment variable NLSPATH and protection of /usr/lib/ifcore_msg.cat.
    ABAQUS Error: ABAQUS/CAE Kernel exited with an error.

    I have not installed Intel fortran and C++ Compilers, since I do not need them at the moment.

    Any suggestion?

    Dimitris

  2. Mike Renfro | May 10, 2007 at 8:51 am | Permalink

    No compilers here, either.

    I remember running into the relFile error on previous Debian releases, but not this time. But I’ve not yet tried it outside amd64, or on lenny.

    When I just now ran CAE, I got the same libgcc error, which I fixed by just renaming the Abaqus libgcc and letting the system libgcc take over.

    As far as the forrtl error, I don’t get that (or any errors except for a harmless missing /sbin/lspci) when I ran CAE just now. The Abaqus system was an Etch amd64 server, and the X display was on an Ubuntu i386 workstation. Both of these are fresh installs, perhaps there’s something in a configuration file in your home directory that’s causing a problem?

  3. Dimitrios Eftaxiopou | May 18, 2007 at 8:20 am | Permalink

    Hi again,
    I tried several things for days, but the fortran error is still there. I even installed an evaluation version of the Intel fortran compiler, but it didn’tmake any difference.

    However the older version ABAQUS 6.5 was installed on lenny and ABAQUS CAE opened with the warning

    X Error: code 155 major 143 minor 5: GLXBadContext.

    Warning: Your system needs to be reconfigured to allow OpenGL
    rendering to a pixmap or PBuffer; otherwise, you will not be
    able to print or use the probe function in ABAQUS/Viewer.

    CAE works apart from the probe function (touch nodes with the mouse pointer and see the results on the picked node). Perhaps a library is not installed.

    Dimitris

  4. Mike Renfro | May 19, 2007 at 2:01 pm | Permalink

    I know CAE requires some level of OpenGL or GLX support in your X server. In my one test case above, I used an Ubuntu 7.04 desktop with ATI FGLRX drivers installed, and had no problems. I don’t plan on doing anything with lenny until much further along in its development cycle.

  5. Dimitrios Eftaxiopou | June 1, 2007 at 4:57 am | Permalink

    The solution to the Xerror is to run abaqus cae with the -mesa option

    abaqus cae -mesa

  6. Mike Renfro | June 1, 2007 at 8:34 am | Permalink

    Right. I had forgotten about the -mesa flag — we ran into the same problem when running Abaqus to a remote X display managed by Hummingbird Exceed on Windows.

  7. AlexVader | January 20, 2008 at 3:13 pm | Permalink

    Hi Mike,

    I have found this blog rather interesting, since, I am trying to install Abaqus 6.7-1 in a Debian family distro;

    I finally got the courage to install Ubuntu in my DualBooter laptop.
    On first impression i may say that Gutsy scored quite well, its a bit weird but, reckoned all my hardware out of the box… i have an Asus F3Jr.

    The issue is that although i can install most of my engineering software over Ubuntu 7.10, CFD codes, Matlab, Ansys, i still cannot install Abaqus over it, and i am starting to like this distro ( Ubuntu Adiction Syndrome :-D hahahah )

    Anyway,

    1. I installed all the shells from synaptics so that i could launch the installer,
    2 I installed termcap packages so that the doc installer wouldn’t complain,
    3 After having intalled the documentation, I launche the doc server.
    4 proceeded to install the application WITHOUT making any upgrade in Gutsy, and
    5 installed the app with the –nosystemcheck option, since Gutsy is not a supported distro.
    6 Installed the License manager
    7 started the LM,
    8 Intalled the Abaqus product.

    when i launch /usr/local/abaqus/command/abaqus , it allows me to define a job, and runs it, but when i launch /usr/local/abaqus/command/abaqus cae, the application crashes with a cae kernel error.

    So… could you pleas tell me what have i done wrong…?
    Some ppl state that it is possible to run Abaqus 6.7-1 in interactive mode under Ubuntu 7.10, and i really would love to be able to quit MS W”#$5&/Z once and for all… it all depends on being able to work with my tools in Linux…. and Abaqus is the most important one… :-D

    Thanks for your time :-)

    Alex

  8. AlexVader | January 20, 2008 at 7:00 pm | Permalink

    Hi again,

    By the way Mike,

    Should you answer to my comment, pls do it to this mail i am using now…

    The other one (bakali_1st@…) is rather spammy… and i am afraid of carelessly having already deleted any reply…

    Thanks again…

    Alex

  9. Mike Renfro | January 22, 2008 at 10:30 am | Permalink

    Alex, I was going to point you to this thread on Ubuntuforums that another person having trouble with Ubuntu pointed me at, but I see you’re already there, and talking to him already.

    But I’ll tell you the same basic things I told him: I don’t have any Ubuntu later than 7.04, and I’d guess that your error either has to do with the Compiz problem he had, or with OpenGL. I have the ATI drivers loaded on the Ubuntu system I manage, and CAE appears to work fine. The -mesa flag should also work on most any X server, but obviously the graphics won’t be as responsive if you’re trying to do major 3D renderings.

    But the majority of my Abaqus users fall into two categories: 1) Windows users, 2) people who submit Abaqus jobs into our compute nodes. I’m not even much of an Abaqus user myself.

    I honestly only wrote up this page originally so that anyone trying to do an amd64 install wouldn’t get as irritated as I did hacking around their inapplicable system checks, and wondering why on earth they’d attach a binary to the end of a shell script, of all things.

  10. AlexVader | January 22, 2008 at 4:01 pm | Permalink

    Thx for your answer :-)

    Ok, now that i have made all upgrades, i’ll give it one more try…

    One different question now…:

    Since you are an experienced engineer/designer what would you advise me to use as a FEA tool?
    Abaqus or Ansys Multiphyscis ?
    Which one do you think is the best… ?

    Alex

  11. Mike Renfro | January 22, 2008 at 7:08 pm | Permalink

    I’m not that experienced, really. Most of my interaction is in helping students get their models built. But it seems that the FEA specialists here tend to end up using Abaqus, and that matches a much earlier experience I saw when I was on co-op at Oak Ridge National Laboratory many years ago. Regular B.S. engineers used ANSYS, COSMOS, or whatever, since most of their time was spent doing CAD and design work. The M.S. and PhD guys that were full-time in FEA used Abaqus. Make of that what you will.

  12. vinod | August 11, 2008 at 11:13 pm | Permalink

    I am getting an error while starting Abaqus CAE
    “The desired vendor daemon is down.
    Check the lmgrd log file, or try lmreread.
    Feature: cae
    Vendor:Host: zenith-0f7013bc
    License path: 27003@zenith-0f7013bc
    FLEXnet Licensing error:-97,121
    For further information, refer to the ABAQUS Installation and Licensing Guide,
    or contact your ABAQUS Inc. representative.
    ABAQUS Error: ABAQUS/CAE Kernel exited with an error.”
    Kindly Help to solve the problem.

  13. Mike Renfro | August 12, 2008 at 10:11 am | Permalink

    To put it simply, host zenith-0f7013bc isn’t running an Abaqus license server on port 27003. Maybe it should be, or maybe the license server is on a different system entirely.

    If you’re not the first Abaqus installation at your location, then find out who’s done the previous installations, and ask them what they used for the license server. This error isn’t specific to amd64, Debian, or any particular version of Abaqus. It’s not even specific to Abaqus.

  14. Jin Park | October 23, 2008 at 6:40 pm | Permalink

    Vinod,
    Did you ever solve your problem?
    JIn

  15. Carter | November 16, 2008 at 7:25 pm | Permalink

    vinod and Jin Park, have you guys solved the problem? I got the same thing when I run Abaqus CAE 6.7.1

    I am using an IBM computer, Win XP Professional.

    qqiangg@yahoo.com is my email, thanks

  16. Carter | November 16, 2008 at 7:26 pm | Permalink

    Mike Renfro,

    Do you know the contact info of Jin Park and Vinod?

    Thanks

  17. Mike Renfro | November 16, 2008 at 9:33 pm | Permalink

    Since they didn’t post their email addresses publicly as you did for yours, I don’t plan on changing that for them without their consent.

    But regardless, my answer should be correct. If this isn’t your company’s or university’s first Abaqus install, then you should be able to contact whoever did the previous ones to find out the license server information. If this is your first install, then whoever bought it should have a contact at Abaqus to get the necessary license information for the designated license server. I’m pretty sure every new Abaqus purchase includes some amount of installation support from the HKS, Dassault, or whoever they are today.

  18. Zaraki | December 7, 2008 at 9:52 pm | Permalink

    Is it me or does everyone find Abaqus help as absolutely useless…… First of all no help or documentation on product is available free of cost and then that documentation even though is vast is a huge jargon which does not help you sort out the problems.. I cant believe Abaqus is from dassault systems which has made user friendly Solidworks

  19. Pinaki | May 28, 2009 at 6:30 pm | Permalink

    Zaraki, you are bang on. Some things about it are absolutely third rate. For example:
    1. Lack of examples. In a manual. Can you believe that?
    2. Figures in the manual are so awfully tiny that in the best case you can’t see them at all. In the worst case, you mistake it for something else, and spend a day figuring it out.
    3. The cyclical references in the beginning of each section. Why couldn’t they make self-contained sections?

  20. h | June 13, 2009 at 10:00 am | Permalink

    i dont know inistiling abaqus

  21. abq302 | April 19, 2010 at 2:06 pm | Permalink

    Hi Dimitrios Eftaxiopou,

    I had similar problem to open abaqus from grid computer and my problem got solved with -mesa flag, abaqus cae -mesa, but the display is very slow, each movement takes ages to load on the screen. I have NVIDIA card. Is there any thing we can do to improve the display loading on the screen.

    Thank you,

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  1. [...] a bit of googling, I discovered this post which gave an explanation of the problem along with a solution. The important part is [...]

  2. nptl | April 6, 2010 at 11:19 pm | Permalink

    [...] have wanted to know the differece between the old threading model and the NPTL threading model. …Mike Renfro's Blog : Abaqus 6.6 on Debian Etch (amd64 port)check libc to see if it was compiled with NPTL – nptl=`strings /lib/libc.so.6 | grep -i nptl` – if [ [...]

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