diff -r a55f2523b53c -r f6bbc0348c44 src/sim/process.cc
--- a/src/sim/process.cc	Fri Aug 28 14:31:03 2015 -0500
+++ b/src/sim/process.cc	Sat Aug 29 10:53:21 2015 -0500
@@ -335,6 +335,18 @@
     // Search through the input options and set fd if match is found;
     // otherwise, open an input file and seek to location.
     FDEntry *fde_stdin = getFDEntry(STDIN_FILENO);
+
+    // Check if user has specified a different input file, and if so, use it
+    // instead of the file specified in the checkpoint. This also resets the
+    // file offset from the checkpointed value
+    string new_in = ((ProcessParams*)params())->input;
+    if (new_in != fde_stdin->filename) {
+        warn("Using new input file (%s) rather than checkpointed (%s)\n",
+             new_in, fde_stdin->filename);
+        fde_stdin->filename = new_in;
+        fde_stdin->fileOffset = 0;
+    }
+
     if ((it = imap.find(fde_stdin->filename)) != imap.end()) {
         fde_stdin->fd = it->second;
     } else {
@@ -345,6 +357,18 @@
     // Search through the output/error options and set fd if match is found;
     // otherwise, open an output file and seek to location.
     FDEntry *fde_stdout = getFDEntry(STDOUT_FILENO);
+
+    // Check if user has specified a different output file, and if so, use it
+    // instead of the file specified in the checkpoint. This also resets the
+    // file offset from the checkpointed value
+    string new_out = ((ProcessParams*)params())->output;
+    if (new_out != fde_stdout->filename) {
+        warn("Using new output file (%s) rather than checkpointed (%s)\n",
+             new_out, fde_stdout->filename);
+        fde_stdout->filename = new_out;
+        fde_stdout->fileOffset = 0;
+    }
+
     if ((it = oemap.find(fde_stdout->filename)) != oemap.end()) {
         fde_stdout->fd = it->second;
     } else {
@@ -353,6 +377,18 @@
     }
 
     FDEntry *fde_stderr = getFDEntry(STDERR_FILENO);
+
+    // Check if user has specified a different error file, and if so, use it
+    // instead of the file specified in the checkpoint. This also resets the
+    // file offset from the checkpointed value
+    string new_err = ((ProcessParams*)params())->errout;
+    if (new_err != fde_stderr->filename) {
+        warn("Using new error file (%s) rather than checkpointed (%s)\n",
+             new_err, fde_stderr->filename);
+        fde_stderr->filename = new_err;
+        fde_stderr->fileOffset = 0;
+    }
+
     if (fde_stdout->filename == fde_stderr->filename) {
         // Reuse the same file descriptor if these match.
         fde_stderr->fd = fde_stdout->fd;