14 Replies Latest reply on Sep 4, 2013 2:52 PM by juaneco2710

    Segmentation fault during openf90 compile

    efluder

      While compiling the AMBER 11 MD program, the compiler failed with the following message. Any work-around?

      Code compiles cleanly with gfortran and ifort

      Gene

       

       

      Signal: Segmentation fault in IR->WHIRL Conversion phase.

      "_pb_exmol.f": Error: Signal Segmentation fault in phase IR->WHIRL Conversion -- processing aborted

      *** Internal stack backtrace:

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x810df36]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x810efab]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x810ec92]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x810ed0d]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x810f5f1]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x806d13c]

          [0x55555400]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x80cc0f4]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x80ce82a]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x82fd9f7]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x82fb454]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x82fe247]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x8309b68]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x8309e98]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x830a293]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x811a198]

          /lib/libc.so.6(__libc_start_main+0xe6) [0x4a6ce6]

          /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95() [0x805ce41]

      openf90 INTERNAL ERROR: /packages/x86_open64/4.5.1-1/lib/gcc-lib/x86_64-open64-linux/4.5.1/mfef95 died due to signal 4

        • Re: Segmentation fault during openf90 compile
          santosh.zanjurne

          I am in the process of getting Amber11 sources; in the mean time would it be possible for you to give me a preprocessed file or a test case with command line used which would reproduced this problem? Other details like OS-name-version will be helpful.

           

          Regards,

          Santosh

            • Re: Segmentation fault during openf90 compile
              efluder

              Santosh,

               

              I sent off a request to the AMBER folks for permission to send you the offending subroutine and the supporting .mod files. If you get the source, the file in question is AmberTools/src/pbsa/pb_exmol.f

               

              I've tried to get a snippet that would exhibit the failure but no luck so far.

               

              Operating system is CentOS 6.2

               

              Command line is:  openf90 -c -O3  -freeform   -o pb_exmol.o pbexmol.f

               

              The segfault occurs regardless of optimization level.

               

              Regards,

              Gene

              -- Eugene M Fluder, Jr, PhD

              Computational Scientist

              Scientific Computing

               

              The Mt. Sinai School of Medicine

              One Gustave L. Levy Place, Box 1498

              New York, NY 10029-6574

               

              T: 212 659 8608

              F: 646 537 8660

              E: eugene.fluder@mssm.edu

                  • Re: Segmentation fault during openf90 compile
                    efluder

                    I've got permission to send you the routine. I've got a tar ball. Where should I send it?

                    Gene

                      • Re: Segmentation fault during openf90 compile
                        santosh.zanjurne

                        Hi Eugene,

                        We have new version of the Open64 compiler, v4.5.2, released with performance improvements and many bug fixes.  The issue you reported has also been fixed.  Please check.

                         

                        For defails refer http://developer.amd.com/tools/open64/pages/default.aspx

                         

                        Regards,

                        Santosh

                          • Re: Segmentation fault during openf90 compile
                            yetilab

                            Hello Santosh,

                             

                            I see the same error message when trying to compile VASP (http://www.vasp.at/):

                             

                               openf95  -c wave.f90

                               Signal: Segmentation fault in IR->WHIRL Conversion phase.

                               "wave.f90": Error: Signal Segmentation fault in phase IR->WHIRL Conversion -- processing aborted

                             

                            (Intel's compiler 12.1 is working fine.)

                             

                            I am  using open64 with version 4.5.2.

                            Ulf

                              • Re: Segmentation fault during openf90 compile
                                santosh.zanjurne

                                Hello Ulf,

                                I dont have license to use VASP.

                                 

                                Would it be possible for you to give me a testcase?  Give me a backtrace also, some times this alone can help.  Also i would need the details like OS name-gcc-binutil version.  How you are using the Open64 compiler binaries i.e. You are building from the sources or which tar/rpm you downloaded?

                                 

                                Regards,

                                Santosh

                                  • Re: Segmentation fault during openf90 compile
                                    santosh.zanjurne

                                    Since the AMBER problem is fixed and is not reproducible with latest compiler binaries, your problem looks to be different or same as AMBER but reproducible in some other enviornment than what we have now.  If would help us fix this if you give me more information about your compilation enviornment.  Hoping to here back from you soon.

                                     

                                    Regards,

                                    Santosh

                                      • Re: Segmentation fault during openf90 compile
                                        kvaibhav

                                        Hello Santosh,

                                         

                                        I am facing the same problem. I am trying to compile vasp on Centos 6.2.

                                        Here is the detailed description.

                                         

                                        Open64: 4.5.2

                                        gcc -v : 4.4.6 20110731

                                         

                                        Here is the back trace:

                                         

                                        "wave.f90": Error: Signal Segmentation fault in phase IR->WHIRL Conversion -- processing aborted

                                        *** Internal stack backtrace:

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4c4bc6]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4c5cef]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4c5aaf]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4c6398]

                                            /lib64/libc.so.6() [0x3b7ce32900]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x48f4e7]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4b4e41]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x6a35fc]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x697b18]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x69a8d0]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x6a7112]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x6a7466]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x6a78a0]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x4cf64b]

                                            /lib64/libc.so.6(__libc_start_main+0xfd) [0x3b7ce1ecdd]

                                            /usr/local/x86_open64-4.5.2/lib/gcc-lib/x86_64-open64-linux/4.5.2/mfef95() [0x41b5c9]

                                          • Re: Segmentation fault during openf90 compile
                                            santosh.zanjurne

                                            Hello Vaibhav,

                                            I am still trying to see if i could locate the problem but it can done faster if you could help me with some reproducible or a testcase.  It should not very time consuming also, what you will have to do is to narrow down the subroutine in the .f90 file and then see what type of code is causing the failure.

                                             

                                            If not you can report this proeblm to vasp team and get their help in this.

                                             

                                            Regards,

                                            Santosh

                                              • Re: Segmentation fault during openf90 compile
                                                kvaibhav

                                                Hi Santosh,

                                                 

                                                As you have suggested I tried to narrow down to the procedure which is giving error.

                                                 

                                                Since the compiler iteself is failing in compiling vasp code so you need to have vasp source with you.

                                                since it is a commercial code I cannot redistribute it.

                                                 

                                                Compiler crashes while compiling wave.f90 file.

                                                I found out that at line 372 of wave.f90 'use pseudo' is having problem.

                                                On checking the psuedo.f90 I found the error is in line 172-181

                                                      INTERFACE

                                                      FUNCTION PP_POINTER(P, NI, NT)

                                                        USE pseudo_struct

                                                        IMPLICIT NONE

                                                        TYPE (potcar),TARGET :: P(:)

                                                        INTEGER :: NI      ! ion index

                                                        INTEGER :: NT      ! type index

                                                        TYPE (potcar), POINTER :: PP_POINTER

                                                      END FUNCTION PP_POINTER

                                                      END INTERFACE

                                                 

                                                I am trying to do openf90 -c pseudo.f90; openf90 -c wave.f90

                                                 

                                                Hope this helps you.

                                                Regards

                                                Vaibhav

                                            • Re: Segmentation fault during openf90 compile
                                              juaneco2710

                                              It wasn't clear to me how you solved this problem. I am having the same problem as all these people. I am trying to compile in a cluster at my university. The system has Rocks 6.0. and I get this message:

                                              Signal: Segmentation fault in IR->WHIRL Conversion phase.

                                              "main.f90": Error: Signal Segmentation fault in phase IR->WHIRL Conversion -- processing aborted

                                              *** Internal stack backtrace:

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4c4bf6]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4c5d1f]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4c5adf]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4c63c8]

                                                  /lib64/libc.so.6() [0x3c38632920]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4978ec]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x498e15]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x699e7e]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x69a929]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x6a7142]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x6a78d0]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x4cf67b]

                                                  /lib64/libc.so.6(__libc_start_main+0xfd) [0x3c3861ecdd]

                                                  /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95() [0x41b5c9]

                                              openf95 INTERNAL ERROR: /share/apps/open64/4.5.2.1/lib/gcc-lib/x86_64-open64-linux/4.5.2.1/mfef95 died due to signal 4

                                               

                                              What is strange is that I compiled the same code successfully in my personal computer using Open64 5.0. I am guessing this is a bug, but I was wondering if there is a workaround.

                                               

                                              Thanks. Juan Diego.

                                            • Re: Segmentation fault during openf90 compile
                                              yetilab

                                              Hello Santosh,

                                               

                                              I dont have license to use VASP.

                                              Would it be possible for you to give me a testcase?  Give me a backtrace

                                              also, some times this alone can help.

                                              I have just ask the VASP developers to help us here. I guess we will

                                              have an answer within the next few hours.

                                               

                                              Also i would need the details like OS

                                              SLES 11 SP 1

                                               

                                              > name-gcc-binutil version.

                                              gcc (SUSE Linux) 4.3.4

                                               

                                              How you are using the Open64 compiler

                                              binaries i.e. You are building from the sources or which tar/rpm you

                                              downloaded?

                                              Yes, it is a normal makefile based build.

                                               

                                              Even -O0 dos not help

                                               

                                              Thank you,

                                              Ulf

                                              --