reduce orbit trailer size to 512 to be compatible with new firmware

reduce orbit trailer size to 512 (from 544) to be compatible with new firmware which has only 16 frames in the trailer (necessary for "fat packet" fix)

scripts/runFileTest.sh

 #!/bin/bash
+
+function scdaq_test {
+    echo "Starting scdaq test with GMT P5 capture file: check for crash"
+    timeout 10s src/scdaq --config test/config/scdaq-gmt.conf | uniq -uc
+    GMTRET="${PIPESTATUS[0]}"
+    echo "#############################################################################"
+    echo "Starting scdaq test with CALO P5 capture file: check for crash"
+    timeout 10s src/scdaq --config test/config/scdaq-calo.conf | uniq -uc
+    CALORET="${PIPESTATUS[0]}"
+    if [[ "$GMTRET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
+        echo "SCDAQ test for GMT failed with exit code ${GMTRET}!"
+        GMT_FAILED=true
+    elif [ $(find test/data -name "*scout_GMT*" | wc -l) -eq 0 ] && [ $OUTPUT_EXPECTED = "true" ]; then
+        echo "SCDAQ test for GMT failed, no output files found!"
+        GMT_FAILED=true
+    fi
+    if [[ "$CALORET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
+        echo "SCDAQ test for CALO failed with exit code ${CALORET}!"
+        CALO_FAILED=true
+    elif [ $(find test/data -name "*scout_CALO*" | wc -l) -eq 0 ] && [ $OUTPUT_EXPECTED  = "true" ]; then
+        echo "SCDAQ test for CALO failed, no output files found!"
+        CALO_FAILED=true
+    fi
+}
+
 echo "building scdaq locally"
 cd src
 make all
 cd -
-echo "building scdaq locally"
 cd test/data
 tar -xzvf calo_testfile.tar.gz
 tar -xzvf gmt_testfile.tar.gz
 cd ../../
-echo "Starting scdaq test with GMT P5 capture file: check for crash"
-timeout 20s src/scdaq --config test/config/scdaq-gmt.conf | uniq
-GMTRET="${PIPESTATUS[0]}"
-echo "#############################################################################"
-echo "Starting scdaq test with CALO P5 capture file: check for crash"
-timeout 60s src/scdaq --config test/config/scdaq-calo.conf | uniq
-CALORET="${PIPESTATUS[0]}"
-if [[ "$GMTRET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
-    echo "SCDAQ test for GMT failed with exit code ${GMTRET}!"
-    GMT_FAILED=true
-elif [[ $(find test/data -name "*scout_GMT*" | wc -l) -eq 0 ]]; then
-    echo "SCDAQ test for GMT failed, no output files found!"
-    GMT_FAILED=true
-fi
-if [[ "$CALORET" -ne 124 ]]; then # We expect to fail with a timeout because scdaq isn't supposed to return.
-    echo "SCDAQ test for CALO failed with exit code ${CALORET}!"
-    CALO_FAILED=true
-elif [[ $(find test/data -name "*scout_CALO*" | wc -l) -eq 0 ]]; then
-    echo "SCDAQ test for CALO failed, no output files found!"
-    CALO_FAILED=true
-fi
+OUTPUT_EXPECTED=false
+scdaq_test
+echo "Starting second set of test files"
+echo $GMT_FAILED
+echo $CALO_FAILED
+
+OUTPUT_EXPECTED=true
+cd test/data
+rm calo_testfile.dat
+rm gmt_testfile.dat
+tar -xzvf calo_testfile_mod.tar.gz
+tar -xzvf gmt_testfile_mod.tar.gz
+rm ../test/data/run000000/in_progress/*
+cd ../../
+#next line needed because older GMT files were taken with 5 orbits per packet 
+sed -i 's/nOrbitsPerPacket:1/nOrbitsPerPacket:5/' test/config/scdaq-gmt.conf
+scdaq_test
+
+echo $GMT_FAILED
+echo $CALO_FAILED
 
 if [[ $GMT_FAILED = true || $CALO_FAILED = true ]]; then
     exit 1