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MED function error.

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  • jasonschnell@rocketmail.com
    Dear Frank, We are experiencing segmentation faults in recent versions of NMRPipe on Mac OS X (10.6.8) when using the MED function. An example 2D processing
    Message 1 of 2 , Jul 3, 2012
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      Dear Frank,

      We are experiencing segmentation faults in recent versions of NMRPipe on Mac OS X (10.6.8) when using the MED function. An example 2D processing script is below, and the resulting error message below that. If the line with the MED function is commented out it runs fine.

      Any help on this would be greatly appreciated.

      Best regards,
      Jason

      ------------


      #!/bin/csh

      bruk2pipe -in ./ser \
      -bad 0.0 -aswap -DMX -decim 3400 -dspfvs 20 -grpdly 67.9854736328125 \
      -xN 2048 -yN 128 \
      -xT 1024 -yT 64 \
      -xMODE DQD -yMODE Echo-AntiEcho \
      -xSW 5882.353 -ySW 3772.161 \
      -xOBS 500.012 -yOBS 125.730 \
      -xCAR 4.719 -yCAR 22.722 \
      -xLAB 1H -yLAB 13C \
      -ndim 2 -aq2D States \
      -out ./test.fid -verb -ov

      sleep 1

      nmrPipe -in ./test.fid \
      | nmrPipe -fn SP -off 0.48 -end 1.00 -pow 1 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 150.0 -p1 0 -di \
      | nmrPipe -fn EXT -x1 1.2ppm -xn 0.6ppm -sw \
      | nmrPipe -fn TP \
      \
      | nmrPipe -fn SP -off 0.48 -end 1.00 -pow 1 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -auto \
      | nmrPipe -fn PS -p0 90.0 -p1 0.0 -di \
      | nmrPipe -fn MED -nw 24 \
      | nmrPipe -fn EXT -x1 12.0ppm -xn 27.0ppm -sw \
      | nmrPipe -fn TP \
      -ov -verb -out ./test.ft2

      ------------


      NMRPipe Abort Signal: 11 -1073758752
      NMRPipe System Message: Undefined error: 0
      NMRPipe Signal Message: Segmentation fault
      NMRPipe Error Status: 1
      NMRPipe Function MED
      DATAIO File Write Error 32.
      Request: 512 Actual: -1.
      SYSWRITE Message: Broken pipe
      NMRPipe Process Error, row 21.
      NMRPipe Error processing stream.
      NMRPipe Error Status: 1
      NMRPipe Function PS
      DATAIO File Write Error 32.
      Request: 512 Actual: -1.
      SYSWRITE Message: Broken pipe
      NMRPipe Process Error, row 38.
      NMRPipe Error processing stream.
      NMRPipe Error Status: 1
      NMRPipe Function FT
      DATAIO File Write Error 32.
      Request: 512 Actual: -1.
      SYSWRITE Message: Broken pipe
      NMRPipe Process Error, row 55.
      NMRPipe Error processing stream.
      NMRPipe Error Status: 1
      NMRPipe Function ZF
      DATAIO File Write Error 32.
      Request: 256 Actual: -1.
      SYSWRITE Message: Broken pipe
      NMRPipe Process Error, row 88.
      NMRPipe Error processing stream.
      NMRPipe Error Status: 1
      NMRPipe Function SP SINE
    • delaglio@nmrscience.com
      Hi Jason, Thanks very much for bringing this problem to my attention ... sorry, I (yes, even I) made what we call in the trade a + 1 - 1 kind of mistake
      Message 2 of 2 , Jul 4, 2012
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        Hi Jason,

        Thanks very much for bringing this problem to my attention ... sorry,
        I (yes, even I) made what we call in the trade a "+ 1" "- 1" kind of
        mistake somewhere, but only Mac versions seemed to be troubled.

        A new version of NMRPipe has just been posted, which should fix this.

        Cheerful Regards,

        f

        Quoting "jasonschnell@..." <jason.schnell@...>:

        >
        > Dear Frank,
        >
        > We are experiencing segmentation faults in recent versions of
        > NMRPipe on Mac OS X (10.6.8) when using the MED function. An example
        > 2D processing script is below, and the resulting error message below
        > that. If the line with the MED function is commented out it runs fine.
        >
        > Any help on this would be greatly appreciated.
        >
        > Best regards,
        > Jason
        >
        > ------------
        >
        >
        > #!/bin/csh
        >
        > bruk2pipe -in ./ser \
        > -bad 0.0 -aswap -DMX -decim 3400 -dspfvs 20 -grpdly 67.9854736328125 \
        > -xN 2048 -yN 128 \
        > -xT 1024 -yT 64 \
        > -xMODE DQD -yMODE Echo-AntiEcho \
        > -xSW 5882.353 -ySW 3772.161 \
        > -xOBS 500.012 -yOBS 125.730 \
        > -xCAR 4.719 -yCAR 22.722 \
        > -xLAB 1H -yLAB 13C \
        > -ndim 2 -aq2D States \
        > -out ./test.fid -verb -ov
        >
        > sleep 1
        >
        > nmrPipe -in ./test.fid \
        > | nmrPipe -fn SP -off 0.48 -end 1.00 -pow 1 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 150.0 -p1 0 -di \
        > | nmrPipe -fn EXT -x1 1.2ppm -xn 0.6ppm -sw \
        > | nmrPipe -fn TP \
        > \
        > | nmrPipe -fn SP -off 0.48 -end 1.00 -pow 1 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT -auto \
        > | nmrPipe -fn PS -p0 90.0 -p1 0.0 -di \
        > | nmrPipe -fn MED -nw 24 \
        > | nmrPipe -fn EXT -x1 12.0ppm -xn 27.0ppm -sw \
        > | nmrPipe -fn TP \
        > -ov -verb -out ./test.ft2
        >
        > ------------
        >
        >
        > NMRPipe Abort Signal: 11 -1073758752
        > NMRPipe System Message: Undefined error: 0
        > NMRPipe Signal Message: Segmentation fault
        > NMRPipe Error Status: 1
        > NMRPipe Function MED
        > DATAIO File Write Error 32.
        > Request: 512 Actual: -1.
        > SYSWRITE Message: Broken pipe
        > NMRPipe Process Error, row 21.
        > NMRPipe Error processing stream.
        > NMRPipe Error Status: 1
        > NMRPipe Function PS
        > DATAIO File Write Error 32.
        > Request: 512 Actual: -1.
        > SYSWRITE Message: Broken pipe
        > NMRPipe Process Error, row 38.
        > NMRPipe Error processing stream.
        > NMRPipe Error Status: 1
        > NMRPipe Function FT
        > DATAIO File Write Error 32.
        > Request: 512 Actual: -1.
        > SYSWRITE Message: Broken pipe
        > NMRPipe Process Error, row 55.
        > NMRPipe Error processing stream.
        > NMRPipe Error Status: 1
        > NMRPipe Function ZF
        > DATAIO File Write Error 32.
        > Request: 256 Actual: -1.
        > SYSWRITE Message: Broken pipe
        > NMRPipe Process Error, row 88.
        > NMRPipe Error processing stream.
        > NMRPipe Error Status: 1
        > NMRPipe Function SP SINE
        >
        >
        >
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