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In the end I realized that the PCI-E driver must be first updated to the new version using "aocl install", before the FPGA can be updated with a new binary.
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I had tried this as well, but i did not have any success. The driver installed without a problem and I can see it in the module list with lsmod, but it did not affect the usage of aocl flash.
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It could also be that your shell scripts are being interpreted with dash instead of bash when using /bin/sh.
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I had not tried this yet, so I modified the Intel-supplied flash script that I believe aocl flash executes (located at $AOCL_BOARD_PACKAGE_ROOT/linux64/libexec/flash) to use bash instead of sh, but that did not work either.
I did also notice that the it seems like the change to the flash script may not have been the right file because I still get the same "sh: 1: Syntax error: "(" unexpected" error occasionally, it would be bash throwing the error if I had changed the correct file.
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