lkmc v2-rc

Unsquashed version at v2-rc-unsquashed, but that cannot be merged as it
breaks bisects at several points. All bugs will not bisect to this
humongous change.

It all started with a conversion of the Bash scripts to Python, mainly
because I couldn't stand not being able to properly use --options for
run which has a million options.

Then since that required a full testing, I decided to do all the
refactorings that I had in mind at once, and so I did and it became
v2-rc.

This is the largest patch I have ever done! OMG a few weeks of extra time.
I'm never writing a Bash script for anything that starts getting big again.

Some of the features are:

* separate build-qemu and build-gem5 commands
* common: convert scripts to python. Add --option for everything
* rename build to build-buildroot now that we are splitting all the build
  commands, Linux kernel to follow
* move all git submodules to submodules/ and all buildroot packages to
  packages/
* refactor the out/ structure. Keep projects on toplevel, because guest
  projects separate archs and host ones don't, making a toplevel arch wrong
* do-release: rename to just release
  https://stackoverflow.com/questions/16174992/cant-get-argparse-to-read-quoted-string-with-dashes-in-it
* run: add --terminal and explain gem5 pdb
* just track the lvimrc
* store CLI kernel config fragment inside buildlroot to avoid conflicts
* gem5: document m5 initparam
* readme: make a bunch of things awesomer
* readme: fix broken refs
* parsec-benchmark: update to 75d55ac446a43c47efb1044844a108c6c330184c
  Could not fetch otherwise.
* gem5: M5_OVERRIDE_PY_SOURCE

packages/kernel_modules/user/common.h

@@ -0,0 +1,99 @@
+#ifndef COMMON_H
+#define COMMON_H
+
+#define _XOPEN_SOURCE 700
+#include <fcntl.h> /* open */
+#include <math.h> /* fabs */
+#include <stdint.h> /* uint64_t  */
+#include <stdlib.h> /* size_t */
+#include <stdio.h> /* snprintf */
+#include <sys/types.h>
+#include <unistd.h> /* pread, sysconf */
+#include <stdbool.h>
+
+/* Format documented at:
+ * https://github.com/torvalds/linux/blob/v4.9/Documentation/vm/pagemap.txt
+ */
+typedef struct {
+	uint64_t pfn : 54;
+	unsigned int soft_dirty : 1;
+	unsigned int file_page : 1;
+	unsigned int swapped : 1;
+	unsigned int present : 1;
+} PagemapEntry;
+
+/* Parse the pagemap entry for the given virtual address.
+ *
+ * @param[out] entry      the parsed entry
+ * @param[in]  pagemap_fd file descriptor to an open /proc/pid/pagemap file
+ * @param[in]  vaddr      virtual address to get entry for
+ * @return 0 for success, 1 for failure
+ */
+int pagemap_get_entry(PagemapEntry *entry, int pagemap_fd, uintptr_t vaddr)
+{
+	size_t nread;
+	ssize_t ret;
+	uint64_t data;
+
+	nread = 0;
+	while (nread < sizeof(data)) {
+		ret = pread(
+			pagemap_fd,
+			&data,
+			sizeof(data),
+			(vaddr / sysconf(_SC_PAGE_SIZE)) * sizeof(data) + nread
+		);
+		nread += ret;
+		if (ret <= 0) {
+			return 1;
+		}
+	}
+	entry->pfn = data & (((uint64_t)1 << 54) - 1);
+	entry->soft_dirty = (data >> 54) & 1;
+	entry->file_page = (data >> 61) & 1;
+	entry->swapped = (data >> 62) & 1;
+	entry->present = (data >> 63) & 1;
+	return 0;
+}
+
+/* Convert the given virtual address to physical using /proc/PID/pagemap.
+ *
+ * @param[out] paddr physical address
+ * @param[in]  pid   process to convert for
+ * @param[in] vaddr virtual address to get entry for
+ * @return 0 for success, 1 for failure
+ */
+int virt_to_phys_user(uintptr_t *paddr, pid_t pid, uintptr_t vaddr)
+{
+	char pagemap_file[BUFSIZ];
+	int pagemap_fd;
+
+	snprintf(pagemap_file, sizeof(pagemap_file), "/proc/%ju/pagemap", (uintmax_t)pid);
+	pagemap_fd = open(pagemap_file, O_RDONLY);
+	if (pagemap_fd < 0) {
+		return 1;
+	}
+	PagemapEntry entry;
+	if (pagemap_get_entry(&entry, pagemap_fd, vaddr)) {
+		return 1;
+	}
+	close(pagemap_fd);
+	*paddr = (entry.pfn * sysconf(_SC_PAGE_SIZE)) + (vaddr % sysconf(_SC_PAGE_SIZE));
+	return 0;
+}
+
+bool common_vector_equal(size_t n, double * v1, double * v2, double max_err)
+{
+	double sum = 0.0;
+	double diff;
+	size_t i;
+	for (i = 0; i < n; ++i) {
+		diff = v1[i] - v2[i];
+		sum += diff * diff;
+	}
+	if (sqrt(sum)/n > max_err)
+		return false;
+	return true;
+}
+
+#endif